def setup(self):
global tmp_dir
path = example_hdf5()
seq = Sequence.create('HDF5', path, 'yxt')
self.filepath = os.path.join(tmp_dir, "test_imaging_dataset.sima")
self.ds = ImagingDataset([seq, seq], self.filepath)
self.filepath_tiffs = os.path.join(tmp_dir, "test_dataset_tiffs.sima")
seq = Sequence.create(
'TIFFs', [[example_tiffs(), example_tiffs()],
[example_tiffs(), example_tiffs()],
[example_tiffs(), example_tiffs()],
[example_tiffs(), example_tiffs()]])
self.ds_tiffs = ImagingDataset([seq, seq], self.filepath_tiffs)
def setup(self):
for frame in Sequence.create('HDF5', example_hdf5(), 'yxt'):
break
frame_shifts = [np.array([[[0, 0]], [[-5, -10]]])]
self.frame_shifts = [np.array([[[5, 10]], [[0, 0]]])]
self.correlations = [np.array([[1], [0.9301478]])]
shifted = frame.copy()
shifted = np.roll(shifted, -frame_shifts[0][1, 0, 1], axis=2)
shifted = np.roll(shifted, -frame_shifts[0][1, 0, 0], axis=1)
frames = np.array([frame, shifted])
self.hm2d = hmm.HiddenMarkov2D(n_processes=1, verbose=False)
self.dataset = sima.ImagingDataset(
[Sequence.create('ndarray', frames)], None)
def setup(self):
for frame in Sequence.create('HDF5', example_hdf5(), 'yxt'):
break
frame_shifts = [np.array([[[0, 0]], [[-5, -10]]])]
self.frame_shifts = [np.array([[[5, 10]], [[0, 0]]])]
self.correlations = [np.array([[1], [0.9301478]])]
shifted = frame.copy()
shifted = np.roll(shifted, -frame_shifts[0][1, 0, 1], axis=2)
shifted = np.roll(shifted, -frame_shifts[0][1, 0, 0], axis=1)
frames = np.array([frame, shifted])
self.hm2d = hmm.HiddenMarkov2D(n_processes=1, verbose=False)
self.dataset = sima.ImagingDataset(
[Sequence.create('ndarray', frames)], None)
def parse_channel(channel):
"""Parse an old format channel stored a dictionary
Parameters
----------
channel : dict
Returns
-------
result : sima.Sequence
A sequence equivalent to the old format channel.
"""
_resolve_paths(channel, path)
klass = channel.pop('__class__')
if klass == 'sima.iterables.MultiPageTIFF':
result = Sequence.create('TIFF', channel['path'])
try:
clip = channel['clip']
except KeyError:
clip = None
if clip is not None:
s = (slice(None), slice(None)) + tuple(
slice(*[None if x is 0 else x for x in dim])
for dim in clip)
result = result[s]
elif klass == 'sima.iterables.HDF5':
result = Sequence.create('HDF5', channel['path'],
channel['dim_order'], channel['group'],
channel['key'])
c = channel['dim_order'].index('c')
chan = channel['channel']
s = tuple([
slice(None) if x != c else slice(chan, chan + 1)
for x in range(len(channel['dim_order']))
])
result = result[s]
try:
clip = channel['clip']
except KeyError:
clip = None
if clip is not None:
s = (slice(None), slice(None)) + tuple(
slice(*[None if x is 0 else x for x in dim])
for dim in clip) + (slice(None), )
result = result[s]
else:
raise Exception('Format not recognized.')
return result
def parse_channel(channel):
"""Parse an old format channel stored a dictionary
Parameters
----------
channel : dict
Returns
-------
result : sima.Sequence
A sequence equivalent to the old format channel.
"""
_resolve_paths(channel, path)
klass = channel.pop('__class__')
if klass == 'sima.iterables.MultiPageTIFF':
result = Sequence.create('TIFF', channel['path'])
try:
clip = channel['clip']
except KeyError:
pass
else:
if clip is not None:
s = (slice(None), slice(None)) + tuple(
slice(*[None if x is 0 else x for x in dim])
for dim in clip)
result = result[s]
return result
elif klass == 'sima.iterables.HDF5':
raise Exception('TODO')
else:
raise Exception('Format not recognized.')
def setup(self):
global tmp_dir
self.filepath = os.path.join(tmp_dir, "test_imaging_dataset.sima")
self.tiff_ds = ImagingDataset(
[Sequence.create('TIFF', example_tiff(), 1, 1)],
self.filepath)
def setup(self):
global tmp_dir
path = example_hdf5()
seq = Sequence.create('HDF5', path, 'yxt')
self.filepath = os.path.join(tmp_dir, "test_imaging_dataset.sima")
self.ds = ImagingDataset([seq, seq], self.filepath)
def parse_channel(channel):
"""Parse an old format channel stored a dictionary
Parameters
----------
channel : dict
Returns
-------
result : sima.Sequence
A sequence equivalent to the old format channel.
"""
_resolve_paths(channel, path)
klass = channel.pop('__class__')
if klass == 'sima.iterables.MultiPageTIFF':
result = Sequence.create('TIFF', channel['path'])
try:
clip = channel['clip']
except KeyError:
clip = None
if clip is not None:
s = (slice(None), slice(None)) + tuple(
slice(*[None if x is 0 else x for x in dim])
for dim in clip)
result = result[s]
elif klass == 'sima.iterables.HDF5':
result = Sequence.create(
'HDF5', channel['path'], channel['dim_order'],
channel['group'], channel['key'])
c = channel['dim_order'].index('c')
chan = channel['channel']
s = tuple([slice(None) if x != c else slice(chan, chan + 1)
for x in range(len(channel['dim_order']))])
result = result[s]
try:
clip = channel['clip']
except KeyError:
clip = None
if clip is not None:
s = (slice(None), slice(None)) + tuple(
slice(*[None if x is 0 else x for x in dim])
for dim in clip) + (slice(None),)
result = result[s]
else:
raise Exception('Format not recognized.')
return result
def test_hmm_missing_frame(self):
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
masked_seq = frames.mask([(5, None, None)])
corrected = self.hm2d.correct(
[masked_seq], os.path.join(tmp_dir, 'test_hmm_3.sima'))
assert_(all(np.all(np.isfinite(seq.displacements))
for seq in corrected))
def test_hmm_missing_frame(self):
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
masked_seq = frames.mask([(5, None, None)])
corrected = self.hm2d.correct([masked_seq],
os.path.join(tmp_dir, 'test_hmm_3.sima'))
assert_(
all(np.all(np.isfinite(seq.displacements)) for seq in corrected))
assert_(np.prod(corrected.frame_shape) > 0)
def test_imaging_dataset_3d():
global tmp_dir
path = example_hdf5()
seq = Sequence.create('HDF5', path, 'yxt')
filepath = os.path.join(tmp_dir, "test_imaging_dataset_3d.sima")
ds = ImagingDataset([seq, seq], filepath)
assert_equal((ds.num_sequences, ) + (ds.num_frames, ) + ds.frame_shape,
(2, 40, 1, 128, 256, 1))
def test_imaging_dataset_3d():
global tmp_dir
path = example_hdf5()
seq = Sequence.create('HDF5', path, 'yxt')
filepath = os.path.join(tmp_dir, "test_imaging_dataset_3d.sima")
ds = ImagingDataset([seq, seq], filepath)
assert_equal((ds.num_sequences,) + (ds.num_frames,) + ds.frame_shape,
(2, 40, 1, 128, 256, 1))
def test_hmm_missing_column(self):
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
mask = np.zeros(frames.shape[1:-1], dtype=bool)
mask[:, :, 30] = True
masked_seq = frames.mask([(None, mask, None)])
corrected = self.hm2d.correct(
[masked_seq], os.path.join(tmp_dir, 'test_hmm_3.sima'))
assert_(all(np.all(np.isfinite(seq.displacements))
for seq in corrected))
def test_hmm_missing_column(self):
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
mask = np.zeros(frames.shape[1:-1], dtype=bool)
mask[:, :, 30] = True
masked_seq = frames.mask([(None, mask, None)])
corrected = self.hm2d.correct(
[masked_seq],
os.path.join(tmp_dir, 'test_hmm_missing_column.sima'))
assert_(all(np.all(np.isfinite(seq.displacements))
for seq in corrected))
def __init__(self, path, channel=0, start=0):
app.Canvas.__init__(self, position=(300, 100),
size=(800, 800), keys='interactive')
self.program = gloo.Program(vertex, fragment)
self.program['a_position'] = [(-1., -.5, 0.), (-1., +1.,0.),
(+0.5, -.5, 0.), (+0.5, +1,0.)]
self.program['a_texcoord'] = [(0., 0.), (0., +1),
(+1., 0.), (+1, +1)]
self.program2 = gloo.Program(vertex, fragment)
self.program2['a_position'] = [(-1., -1., 0.), (-1., -0.55,0.),
(+0.5, -1., 0.), (+0.5, -0.55,0.)]
self.program2['a_texcoord'] = [(0., 0.), (0., +1.),
(+1., 0.), (+1., +1.)]
self.program3 = gloo.Program(vertex, fragment)
self.program3['a_position'] = [(0.55, -0.5, 0.), (0.55, +1.,0.),
(+1., -0.5, 0.), (+1., +1.,0.)]
self.program3['a_texcoord'] = [(0., 0.), (0., +1.),
(+1., 0.), (+1., +1.)]
if os.path.splitext(path)[-1] == '.sima':
ds = ImagingDataset.load(path)
self.sequence = ds.__iter__().next()
else:
self.sequence = Sequence.create('HDF5',path,'tzyxc')
self.frame_counter = start
self.step_size = 1
self.channel = channel
self.length = len(self.sequence)
vol = self.sequence._get_frame(self.frame_counter).astype('float32')
vol /= NORMING_VAL
vol = np.clip(vol, 0, 1)
#surf = np.sum(vol,axis=0)[:,:,channel]/vol.shape[0]
surf = np.nanmean(vol,axis=0)[:,:,channel]
self.program['u_texture'] = surf
#surf2 = np.sum(vol,axis=1)[:,:,channel]/vol.shape[1]
surf2 = np.nanmean(vol,axis=1)[:,:,channel]
self.program2['u_texture'] = surf2
#surf3 = np.fliplr((np.sum(vol,axis=2)[:,:,channel]).T)/vol.shape[2]
surf3 = np.fliplr((np.nanmean(vol,axis=2)[:,:,channel]).T)
self.program3['u_texture'] = surf3
self.text = visuals.TextVisual('',font_size=14,color='r',pos=(700, 700))
self.text.text = "{} / {}".format(self.frame_counter, self.length)
self.steptext = visuals.TextVisual('step_size: 1',font_size=10,color='r',pos=(700, 725))
self.tr_sys = visuals.transforms.TransformSystem(self)
self.timer = app.Timer(0.25, connect=self.on_timer, start=True)
def test_hmm_missing_frame(self):
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
masked_seq = frames.mask([(5, None, None)])
with warnings.catch_warnings():
warnings.simplefilter('ignore')
corrected = self.hm2d.correct(
[masked_seq], os.path.join(
tmp_dir, 'test_hmm_missing_frame.sima'))
assert_(all(np.all(np.isfinite(seq.displacements))
for seq in corrected))
assert_(np.prod(corrected.frame_shape) > 0)
def test_hmm_tmp(self): # TODO: remove when displacements.pkl is updated
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
corrected = self.hm2d.correct(
[frames], os.path.join(tmp_dir, 'test_hmm_2.sima'))
with open(misc.example_data() + '/displacements.pkl', 'rb') as fh:
displacements = [d.reshape((20, 1, 128, 2))
for d in pickle.load(fh)]
displacements_ = [seq.displacements for seq in corrected]
assert_(abs(displacements_[0] - displacements[0]).max() <= 1)
def test_hmm(self):
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
corrected = self.hm2d.correct(
[frames], os.path.join(tmp_dir, 'test_hmm.sima'))
with open(misc.example_data() + '/displacements.pkl', 'rb') as fh:
displacements = [d.reshape((20, 1, 128, 2))
for d in pickle.load(fh)]
displacements_ = [seq.displacements for seq in corrected]
assert_almost_equal(displacements_, displacements)
def test_hmm(self):
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
corrected = self.hm2d.correct(
[frames], os.path.join(tmp_dir, 'test_hmm.sima'))
with open(misc.example_data() + '/displacements.pkl', 'rb') as fh:
displacements = [d.reshape((20, 1, 128, 2))
for d in pickle.load(fh)]
displacements_ = [seq.displacements for seq in corrected]
assert_almost_equal(displacements_, displacements)
def test_hmm_tmp(self): # TODO: remove when displacements.pkl is updated
global tmp_dir
frames = Sequence.create('TIFF', example_tiff())
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
corrected = self.hm2d.correct(
[frames], os.path.join(tmp_dir, 'test_hmm_2.sima'))
with open(misc.example_data() + '/displacements.pkl', 'rb') as fh:
displacements = [d.reshape((20, 1, 128, 2))
for d in pickle.load(fh)]
displacements_ = [seq.displacements for seq in corrected]
diffs = displacements_[0] - displacements[0]
assert_(
((diffs - diffs.mean(axis=2).mean(axis=1).mean(axis=0)) > 1).mean()
<= 0.001)
def segment(self, use_settings=False):
"""Performs Spatiotemporal Independent Component Analysis.
Currently only has options to use :class:`sima.segment.STICA`. User is
prompted for parameters necessary to perform stICA. If *use_settings*
is True, the settings from :data:`settings_file` are used instead.
Args:
use_settings (bool, optional): Whether to use the settings stored in
:data:`settings_file`. If False, user is prompted for settings.
"""
if use_settings:
components = int(self.settings['components'])
mu = float(self.settings['mu'])
overlap_per = float(self.settings['overlap_per'])
else:
if self.sequence == None:
prompt = "File path to the image you want to segment (TIFF only): "
input_path = self.getTIFF(prompt)
self.sequence = Sequence.create('TIFF', input_path)
self.dataset = ImagingDataset([self.sequence], self.sima_dir)
prompt = "Number of PCA components (default 50): "
components = self.getNatural(prompt, default=50)
prompt = "mu (default 0.5): "
mu = -1.0
while mu < 0 or mu > 1:
mu = self.getFloat(prompt, default=0.5)
prompt = "Minimum overlap " + \
"(default 20%; enter 0 to skip): "
overlap_per = self.getPercent(prompt, default=0.2)
segment_settings = {
'components': components,
'mu': mu,
'overlap_per': overlap_per,
}
print "Performing Spatiotemporal Independent Component Analysis..."
stdout.flush()
stica = STICA(**segment_settings)
stica.append(IdROIs())
if self.dataset == None:
self.dataset = ImagingDataset.load(self.sima_dir)
self.rois = self.dataset.segment(stica, label="stICA ROIs")
print len(self.dataset.ROIs['stICA ROIs']), "ROIs found"
if not use_settings:
segment_settings['segmentation_strategy'] = 'stICA'
self._updateSettingsFile(segment_settings)
def getChannels(directory):
ds_path = directory.replace(':!', '/')
if (os.path.splitext(ds_path)[-1] == '.sima'):
try:
ds = ImagingDataset.load(ds_path)
except IOError:
return ''
channels = ds.channel_names
else:
try:
seq = Sequence.create('HDF5', ds_path, 'tzyxc')
except IOError:
return ''
channels = ['channel_' + str(idx) for idx in range(seq.shape[4])]
if (len(channels) > 1):
channels += ['overlay']
return render_template('select_list.html', options=channels)
def getChannels(directory):
ds_path = directory.replace(":!", "/")
if os.path.splitext(ds_path)[-1] == ".sima":
try:
ds = ImagingDataset.load(ds_path)
except IOError:
return ""
channels = ds.channel_names
else:
try:
seq = Sequence.create("HDF5", ds_path, "tzyxc")
except IOError:
return ""
channels = ["channel_" + str(idx) for idx in range(seq.shape[4])]
if len(channels) > 1:
channels += ["overlay"]
return render_template("select_list.html", options=channels)
def getInfo():
ds_path = request.form.get('path')
if (os.path.splitext(ds_path)[-1] == '.sima'):
try:
ds = ImagingDataset.load(ds_path)
except IOError:
return jsonify(error='dataset not found')
seq = ds.__iter__().next()
else:
try:
seq = Sequence.create('HDF5', ds_path, 'tzyxc')
except IOError:
return jsonify(error='dataset not found')
length = len(seq)
norm_factors = {}
for channel in xrange(seq.shape[4]):
norm_factors['channel_' + str(channel)] = []
for frame_index in [0, int(length / 2), -1]:
frame = seq._get_frame(frame_index)
for channel in xrange(seq.shape[4]):
subframe = frame[:, :, :, channel]
if np.any(np.isfinite(subframe)):
factor = np.percentile(
subframe[np.where(np.isfinite(subframe))], 98)
if np.isfinite(factor):
norm_factors['channel_' + str(channel)] += [factor]
json = {
'planes': range(int(seq.shape[1] + 1)),
'height': int(seq.shape[2]),
'width': int(seq.shape[3]),
'length': length
}
for channel in norm_factors.keys():
json[channel] = int(max(1, int(np.nanmean(norm_factors[channel]))))
return jsonify(**json)
def getInfo():
ds_path = request.form.get("path")
if os.path.splitext(ds_path)[-1] == ".sima":
try:
ds = ImagingDataset.load(ds_path)
except IOError:
return jsonify(error="dataset not found")
seq = ds.__iter__().next()
else:
try:
seq = Sequence.create("HDF5", ds_path, "tzyxc")
except IOError:
return jsonify(error="dataset not found")
length = len(seq)
norm_factors = {}
for channel in xrange(seq.shape[4]):
norm_factors["channel_" + str(channel)] = []
for frame_index in [0, int(length / 2), -1]:
frame = seq._get_frame(frame_index)
for channel in xrange(seq.shape[4]):
subframe = frame[:, :, :, channel]
if np.any(np.isfinite(subframe)):
factor = np.percentile(subframe[np.where(np.isfinite(subframe))], 98)
if np.isfinite(factor):
norm_factors["channel_" + str(channel)] += [factor]
json = {"planes": range(seq.shape[1] + 1), "height": seq.shape[2], "width": seq.shape[3], "max": length}
for channel in norm_factors.keys():
json[channel] = max(1, int(np.nanmean(norm_factors[channel])))
return jsonify(**json)
def getFrames():
ds_path = request.form.get('path')
requestFrames = request.form.getlist('frames[]', type=int)
normingVal = request.form.getlist('normingVal[]', type=float)
sequenceId = request.form.get('sequenceId')
channel = request.form.get('channel')
planes = request.form.getlist('planes[]', type=int)
cycle = request.form.get('cycle', type=int)
if planes is None:
planes = [0]
quality = 40
if channel == 'overlay':
channel = None
ds = None
if (os.path.splitext(ds_path)[-1] == '.sima'):
ds = ImagingDataset.load(ds_path)
seq = ds.sequences[cycle]
channel = ds._resolve_channel(channel)
else:
seq = Sequence.create('HDF5', ds_path, 'tzyxc')
if channel:
channel = int(channel.split('_')[-1])
end = False
frames = {}
for frame_number in requestFrames:
norming_val = normingVal[:]
if frame_number > len(seq) - 1 or frame_number < -1:
end = True
continue
elif frame_number == -1 and ds is not None:
try:
time_averages = pickle.load(
open(os.path.join(ds.savedir, 'time_averages.pkl')))
if not isinstance(time_averages, np.ndarray):
raise Exception('no time average')
except:
vol = seq._get_frame(0)
else:
vol = ds.time_averages
for ch in xrange(vol.shape[3]):
subframe = vol[:, :, :, ch]
factor = np.percentile(
subframe[np.where(np.isfinite(subframe))], 99)
if np.isfinite(factor):
norming_val[ch] = factor
else:
vol = seq._get_frame(frame_number)
if channel is not None:
vol = vol[:, :, :, channel]
vol /= ((norming_val[channel]) / 255)
vol = np.clip(vol, 0, 255)
else:
vol = np.hstack((vol[:, :, :, 0] / norming_val[0],
vol[:, :, :, 1] / norming_val[1]))
vol *= 255
frames['frame_' + str(frame_number)] = {}
for plane in planes:
if plane == 0:
zsurf = np.nanmean(vol, axis=0)
else:
zsurf = vol[plane - 1, :, :]
if plane == 0:
ysurf = np.nanmean(vol, axis=1)
else:
ysurf = np.zeros((vol.shape[0], vol.shape[2]))
ysurf[plane - 1, :] = np.nanmean(zsurf, axis=0)
if plane == 0:
xsurf = np.nanmean(vol, axis=2).T
else:
xsurf = np.zeros((vol.shape[1], vol.shape[0]))
xsurf[:, plane - 1] = np.nanmean(zsurf, axis=1).T
frames['frame_' + str(frame_number)][plane] = {
'z': convertToB64Jpeg(zsurf.astype('uint8'), quality=quality),
'y': convertToB64Jpeg(ysurf.astype('uint8'), quality=quality),
'x': convertToB64Jpeg(xsurf.astype('uint8'), quality=quality)
}
return jsonify(end=end, sequenceId=sequenceId, **frames)
def motionCorrect(self,
input_path=None,
output_path=None,
use_settings=False):
"""Perform motion correction on a recording and export frames.
Uses settings from :data:`mc_radio` or (if *use_settings* is True)
:data:`settings_file`.
Args:
input_path (str, optional) : File path to the image to be corrected.
If None, user is prompted for location.
output_path (str, optional): File path to export corrected frames. If
None, user is prompted for location.
use_settings (bool, optional): Whether to use the settings stored in
:data:`settings_file`. If False, user is prompted for settings.
"""
# sima uses the builtin input() function, which is not compatible with IPython
if isdir(self.sima_dir):
if ipython_loaded():
msg = "You cannot perform motion correction using an" + \
" existing SIMA analysis directory"
warnings.warn(msg)
return # exit before we screw something up
if input_path == None:
# currently only TIFF is supported by SARA
prompt = "File path to the image you want corrected (TIFF only): "
input_path = self.getTIFF(prompt)
if output_path == None:
prompt = "Where would you like to save the corrected frames? "
self.corrected_frames = self.reserveFilePath(prompt)
else:
self.corrected_frames = output_path
self.sequence = Sequence.create('TIFF', input_path)
if use_settings:
md_x = int(self.settings['max_displacement_x'])
md_y = int(self.settings['max_displacement_y'])
else:
prompt = ["Maximum %s displacement (in pixels; default 100): " \
% ax for ax in ['X', 'Y']]
md_x = self.getNatural(prompt[0], default=100)
md_y = self.getNatural(prompt[1], default=100)
mc_settings = {"max_displacement": [md_x, md_y]}
if use_settings:
strategy = self.settings['correction_strategy']
self._motion_correction_map[strategy](mc_settings)
else:
# By this time, the user should have selected a strategy
self.strategy_radio.close()
self._motion_correction_map[self.strategy_radio.value](mc_settings)
# export settings we used to settings file
mc_settings = {
'uncorrected_image': abspath(input_path),
'corrected_image': abspath(self.corrected_frames),
'max_displacement_x': md_x,
'max_displacement_y': md_y,
'correction_strategy': self.strategy_radio.value,
}
self._updateSettingsFile(mc_settings)
def parse_sequence(sequence):
channels = [parse_channel(c) for c in sequence]
return Sequence.join(*channels)
def getFrames():
ds_path = request.form.get("path")
requestFrames = request.form.getlist("frames[]", type=int)
normingVal = request.form.getlist("normingVal[]", type=float)
sequenceId = request.form.get("sequenceId")
channel = request.form.get("channel")
planes = request.form.getlist("planes[]", type=int)
cycle = request.form.get("cycle", type=int)
if planes is None:
planes = [0]
quality = 40
if channel == "overlay":
channel = None
ds = None
if os.path.splitext(ds_path)[-1] == ".sima":
ds = ImagingDataset.load(ds_path)
seq = ds.sequences[cycle]
channel = ds._resolve_channel(channel)
else:
seq = Sequence.create("HDF5", ds_path, "tzyxc")
if channel:
channel = int(channel.split("_")[-1])
end = False
frames = {}
for frame_number in requestFrames:
norming_val = normingVal[:]
if frame_number > len(seq) - 1 or frame_number < -1:
end = True
continue
elif frame_number == -1 and ds is not None:
try:
time_averages = pickle.load(open(os.path.join(ds.savedir, "time_averages.pkl")))
if not isinstance(time_averages, np.ndarray):
raise Exception("no time average")
except:
vol = seq._get_frame(0)
else:
vol = ds.time_averages
for ch in xrange(vol.shape[3]):
subframe = vol[:, :, :, ch]
factor = np.percentile(subframe[np.where(np.isfinite(subframe))], 99)
if np.isfinite(factor):
norming_val[ch] = factor
else:
vol = seq._get_frame(frame_number)
if channel is not None:
vol = vol[:, :, :, channel]
vol /= (norming_val[channel]) / 255
vol = np.clip(vol, 0, 255)
else:
vol = np.hstack((vol[:, :, :, 0] / norming_val[0], vol[:, :, :, 1] / norming_val[1]))
vol *= 255
frames["frame_" + str(frame_number)] = {}
for plane in planes:
if plane == 0:
zsurf = np.nanmean(vol, axis=0)
else:
zsurf = vol[plane - 1, :, :]
if plane == 0:
ysurf = np.nanmean(vol, axis=1)
else:
ysurf = np.zeros((vol.shape[0], vol.shape[2]))
ysurf[plane - 1, :] = np.nanmean(zsurf, axis=0)
if plane == 0:
xsurf = np.nanmean(vol, axis=2).T
else:
xsurf = np.zeros((vol.shape[1], vol.shape[0]))
xsurf[:, plane - 1] = np.nanmean(zsurf, axis=1).T
frames["frame_" + str(frame_number)][plane] = {
"z": convertToB64Jpeg(zsurf.astype("uint8"), quality=quality),
"y": convertToB64Jpeg(ysurf.astype("uint8"), quality=quality),
"x": convertToB64Jpeg(xsurf.astype("uint8"), quality=quality),
}
return jsonify(end=end, sequenceId=sequenceId, **frames)
def setup(self):
self.strategy = sima.motion.ResonantCorrection(
sima.motion.HiddenMarkov2D(n_processes=1, verbose=False), 5)
self.dataset = sima.ImagingDataset(
[Sequence.create('HDF5', example_volume(), 'tzyxc')], None)
def parse_sequence(sequence):
channels = [parse_channel(c) for c in sequence]
return Sequence.join(*channels)
import matplotlib.pyplot as plt
import nimfa
import scipy
import scipy.sparse
from nitime import utils
from nitime import algorithms as alg
from nitime.timeseries import TimeSeries
#
from PIL import Image
# path ='/Users/Chithra/Documents/Columbia/Semester2/Test/z-series-004/z-series-004_Cycle00001_Element00001.h5'
# path ='/Users/Chithra/Documents/Columbia/Semester2/Test/TSeries-08242014-Day1-SessionA-000/TSeries-08242014-Day1-SessionA-000_Cycle00001_Element00001.h5'
path = '/Users/Chithra/Documents/Columbia/Semester2/NMF/ctxA-002/ctxA-002_Cycle00001_Element00001.h5'
# NORMING_VAL = 2194
options={}
sequence = Sequence.create('HDF5',path,'tzxyc')
print sequence.shape
(T, P, R, C, channel) = sequence.shape
# For testing, only use the first 3
P=1
# R=150
# C=150
T=800
d = R*C #Number of pixels
Y = np.zeros((R,C,T),dtype='float64') #Number of observations
for i in range(0,T):
vol = sequence._get_frame(i).astype('float32')
vol = np.nanmean(vol,axis=3)[0,:,:]
print i
Y[:,:,i] = vol
def setup(self):
global tmp_dir
self.filepath = os.path.join(tmp_dir, "test_imaging_dataset.sima")
self.tiff_ds = ImagingDataset(
[Sequence.create('TIFF', example_tiff(), 1, 1)], self.filepath)
def __init__(self, path, channel=0, start=0):
app.Canvas.__init__(self,
position=(300, 100),
size=(800, 800),
keys='interactive')
self.program = gloo.Program(vertex, fragment)
self.program['a_position'] = [(-1., -.5, 0.), (-1., +1., 0.),
(+0.5, -.5, 0.), (+0.5, +1, 0.)]
self.program['a_texcoord'] = [(0., 0.), (0., +1), (+1., 0.), (+1, +1)]
self.program2 = gloo.Program(vertex, fragment)
self.program2['a_position'] = [(-1., -1., 0.), (-1., -0.55, 0.),
(+0.5, -1., 0.), (+0.5, -0.55, 0.)]
self.program2['a_texcoord'] = [(0., 0.), (0., +1.), (+1., 0.),
(+1., +1.)]
self.program3 = gloo.Program(vertex, fragment)
self.program3['a_position'] = [(0.55, -0.5, 0.), (0.55, +1., 0.),
(+1., -0.5, 0.), (+1., +1., 0.)]
self.program3['a_texcoord'] = [(0., 0.), (0., +1.), (+1., 0.),
(+1., +1.)]
if os.path.splitext(path)[-1] == '.sima':
ds = ImagingDataset.load(path)
self.sequence = ds.__iter__().next()
else:
self.sequence = Sequence.create('HDF5', path, 'tzyxc')
self.frame_counter = start
self.step_size = 1
self.channel = channel
self.length = len(self.sequence)
vol = self.sequence._get_frame(self.frame_counter).astype('float32')
vol /= NORMING_VAL
vol = np.clip(vol, 0, 1)
#surf = np.sum(vol,axis=0)[:,:,channel]/vol.shape[0]
surf = np.nanmean(vol, axis=0)[:, :, channel]
self.program['u_texture'] = surf
#surf2 = np.sum(vol,axis=1)[:,:,channel]/vol.shape[1]
surf2 = np.nanmean(vol, axis=1)[:, :, channel]
self.program2['u_texture'] = surf2
#surf3 = np.fliplr((np.sum(vol,axis=2)[:,:,channel]).T)/vol.shape[2]
surf3 = np.fliplr((np.nanmean(vol, axis=2)[:, :, channel]).T)
self.program3['u_texture'] = surf3
self.text = visuals.TextVisual('',
font_size=14,
color='r',
pos=(700, 700))
self.text.text = "{} / {}".format(self.frame_counter, self.length)
self.steptext = visuals.TextVisual('step_size: 1',
font_size=10,
color='r',
pos=(700, 725))
self.tr_sys = visuals.transforms.TransformSystem(self)
self.timer = app.Timer(0.25, connect=self.on_timer, start=True)
