class SubjectInfo(HasTraits):
physiodata = Instance(PhysioData)
subject_age = DelegatesTo("physiodata")
subject_gender = DelegatesTo("physiodata")
subject_weight = DelegatesTo("physiodata")
subject_height_ft = DelegatesTo("physiodata")
subject_height_in = DelegatesTo("physiodata")
subject_electrode_distance_front = DelegatesTo("physiodata")
subject_electrode_distance_back = DelegatesTo("physiodata")
subject_electrode_distance_right = DelegatesTo("physiodata")
subject_electrode_distance_left = DelegatesTo("physiodata")
subject_resp_max = DelegatesTo("physiodata")
subject_resp_min = DelegatesTo("physiodata")
subject_in_mri = DelegatesTo("physiodata")
subject_control_base_impedance = DelegatesTo("physiodata")
traits_view = MEAPView(
VGroup(Item("subject_age"),
Item("subject_gender"),
Item("subject_height_ft"),
Item("subject_height_in"),
Item("subject_weight"),
Item("subject_electrode_distance_front"),
Item("subject_electrode_distance_back"),
Item("subject_electrode_distance_left"),
Item("subject_electrode_distance_right"),
Item("subject_resp_max"),
Item("subject_resp_min"),
Item("subject_in_mri"),
Item('subject_control_base_impedance'),
label="Participant Measurements"),
buttons=[OKButton],
resizable=True,
win_title="Subject Info",
)
class PreprocessingPipeline(HasTraits):
# Holds the set of multiple acq files
group_excel_file = File
# Which columns contain numeric data?
# Holds the unique eveny types for this experiment
physio_files = List(Instance(PhysioFilePreprocessor))
# Interactively process the data?
interactive = Bool(True)
header = List
@on_trait_change("group_excel_file")
def open_xls(self, fpath=""):
if not fpath:
fpath = self.group_excel_file
logger.info("Loading " + fpath)
wb = xlrd.open_workbook(fpath)
sheet = wb.sheet_by_index(0)
header = [str(item.value) for item in sheet.row(0)]
for rnum in range(1, sheet.nrows):
rw = sheet.row(rnum)
if not len(rw) == len(header):
#raise ValueError("not enough information in row %d" % (rnum + 1))
continue
#convert to numbers and strings
specs = {}
for item, hdr in zip(rw, header):
if hdr == "in_mri":
specs[hdr] = bool(item.value)
else:
try:
specs[hdr] = float(item.value)
except Exception:
specs[hdr] = str(item.value)
self.physio_files.append(
PhysioFilePreprocessor(interactive=self.interactive,
file=specs['file'],
outfile=specs.get('outfile', ''),
specs=specs))
self.header = header
traits_view = MEAPView(VGroup(
VGroup("group_excel_file", show_border=True, label="Excel Files"),
HGroup(Item("physio_files", editor=pipeline_table, show_label=False)),
),
resizable=True,
width=300,
height=500)
class PhysioFilePreprocessor(HasTraits):
# Holds the data from
physiodata = Instance(PhysioData)
interactive = Bool(True)
pipeline = Instance(MEAPPipeline)
file = DelegatesTo("pipeline")
outfile = DelegatesTo("pipeline")
specs = Dict
importer_kwargs = DelegatesTo("pipeline")
mea_saved = Property(Bool, depends_on="file,outfile")
def _outfile_default(self):
if self.file.endswith(".acq"):
return self.file[:-4] + ".mea"
return self.file + ".mea"
def __init__(self, **traits):
super(PhysioFilePreprocessor, self).__init__(**traits)
# Some of the data contained in the excel sheet should get
# attached to the physiodata file once it is loaded. These
# go into the physiodata_kwargs attribute
pd_traits = PhysioData().editable_traits()
for spec, spec_value in self.specs.iteritems():
if "subject_" + spec in pd_traits:
self.importer_kwargs["subject_" + spec] = spec_value
def _pipeline_default(self):
pipeline = MEAPPipeline()
return pipeline
def _get_mea_saved(self):
if self.file.endswith("mea"):
return True
return os.path.exists(self.pipeline.outfile) or \
os.path.exists(self.pipeline.outfile + ".mat")
@on_trait_change("pipeline.saved")
def pipeline_saved(self):
"""A dumb hack"""
old_outfile = self.outfile
self.outfile = "asdf"
self.outfile = old_outfile
pipeline_view = MEAPView(
Group(Item("pipeline", style="custom"), show_labels=False))
class MEAPhysioExperiment(PhysioExperiment):
events = List(Instance(ExpEvent))
physio_files = List(Instance(PhysioFileMEAAnalysis))
def _b_save_fired(self):
raise NotImplementedError()
def file_constructur(self):
return PhysioFileMEAAnalysis
def event_constructor(self):
return MovingEnsembler
def run(self):
# read the excel file
self.open_xls()
# organize all the data from it
if not self.events_processed:
self._process_events()
# Run the pipeline on each acq_file
self.extract_mea()
def extract_mea(self):
stacks = {}
for evt in self.conditions:
stacks[evt] = {}
for pf in self.physio_files:
pf.extract_mea()
def save_mea_document(self, output_path=""):
#self.ensemble_average()
if not output_path:
output_path = self.output_xls
traits_view = MEAPView(HSplit(
Group(
Group(Item("input_path", label="Input XLS"),
Item("output_directory", label="Output Directory"),
Item("b_run", show_label=False),
Item("b_save", show_label=False),
orientation="horizontal"), ), ),
resizable=True,
win_title="MEA Analysis")
class MEAPGreeter(HasTraits):
preproc = Button("Preprocess")
analyze = Button("Analyze")
configure = Button("Configure MEAP")
batch_spreadsheet = Button("Create Batch Spreadsheet")
register_dZdt = Button("Batch Register dZ/dt")
def _preproc_fired(self):
from meap.preprocessing import PreprocessingPipeline
preproc=PreprocessingPipeline()
preproc.configure_traits()
def _analyze_fired(self):
from meap.physio_analysis import PhysioExperiment
pe = PhysioExperiment()
pe.configure_traits()
def _register_dZdt_fired(self):
from meap.batch_warp_dzdt import BatchGroupRegisterDZDT
batch = BatchGroupRegisterDZDT()
batch.configure_traits()
def _batch_spreadsheet_fired(self):
from meap.make_batch_spreadsheet import BatchFileTool
bft = BatchFileTool()
bft.configure_traits()
def _configure_fired(self):
print "Not implemented yet!"
traits_view=MEAPView(
VGroup(
Item("preproc"),
Item("analyze"),
Item("batch_spreadsheet"),
Item("register_dZdt"),
Item("configure"),
show_labels=False
)
)
def default_traits_view(self):
plots = [ Item(sig+"_ts", style="custom", show_label=False) for sig in \
sorted(self.physiodata.contents) if not sig.startswith("resp_corr")]
if "ecg2" in self.physiodata.contents:
widgets = VGroup(
Item("qrs_source_signal", label="ECG to use"),
Item("start_time"),
Item("window_size"),
)
else:
widgets = VGroup(
Item("start_time"),
Item("window_size"),
)
return MEAPView(VGroup(VGroup(*plots),
Group(widgets, orientation="horizontal")),
width=1000,
height=600,
resizable=True,
win_title="Aqcknowledge Data",
buttons=[OKButton, CancelButton],
handler=DataPlotHandler())
class CensorRegion(HasTraits):
start_time = Float(-1.)
end_time = Float(-1.)
viz = Instance(RangeSelectionOverlay, transient=True)
metadata_name = Str
plot = Instance(LinePlot, transient=True)
traits_view = MEAPView(Item("start_time"), Item("end_time"))
def set_limits(self, start, end):
"""
"""
self.plot.index.metadata[self.metadata_name] = start, end
@on_trait_change("plot.index.metadata")
def metadata_chaned(self):
try:
if self.plot.index.metadata[self.metadata_name] is None:
return
st, end = self.plot.index.metadata[self.metadata_name]
except KeyError:
return
self.start_time = st
self.end_time = end
def _viz_default(self):
self.plot.active_tool = CensorSelection(
self.plot,
selection_mode="append",
append_key=KeySpec("control"),
left_button_selects=True,
metadata_name=self.metadata_name)
rso = RangeSelectionOverlay(component=self.plot,
metadata_name=self.metadata_name)
self.plot.overlays.append(rso)
return rso
class RespirationProcessor(HasTraits):
# Parameters
resp_polort = DelegatesTo("physiodata")
resp_high_freq_cutoff = DelegatesTo("physiodata")
time = DelegatesTo("physiodata", "processed_respiration_time")
# Data object and arrays to save
physiodata = Instance(PhysioData)
respiration_cycle = DelegatesTo("physiodata")
respiration_amount = DelegatesTo("physiodata")
# For visualization
plots = Instance(VPlotContainer, transient=True)
# Respiration plot
resp_plot = Instance(Plot, transient=True)
resp_plot_data = Instance(ArrayPlotData, transient=True)
resp_signal = Array() # Could be filtered z0 or resp belt
raw_resp_signal = Array() # Could be filtered z0 or resp belt
resp_signal = Property(
Array,
depends_on="physiodata.resp_polort,physiodata.resp_high_freq_cutoff")
polyfilt_resp = Array()
lpfilt_resp = DelegatesTo("physiodata", "processed_respiration_data")
resp_inhale_begin_times = DelegatesTo("physiodata")
resp_inhale_begin_values = Array
resp_exhale_begin_times = DelegatesTo("physiodata")
resp_exhale_begin_values = Array
z0_plot = Instance(Plot, transient=True)
z0_plot_data = Instance(ArrayPlotData, transient=True)
raw_z0_signal = Array()
resp_corrected_z0 = DelegatesTo("physiodata")
dzdt_plot = Instance(Plot, transient=True)
dzdt_plot_data = Instance(ArrayPlotData, transient=True)
raw_dzdt_signal = Array()
resp_corrected_dzdt = DelegatesTo("physiodata")
start_time = Range(low=0, high=10000.0, initial=0.0)
window_size = Range(low=1.0, high=300.0, initial=30.0)
state = Enum("unusable", "z0", "resp", "z0_resp")
dirty = Bool(True)
b_process = Button(label="Process Respiration")
def __init__(self, **traits):
super(RespirationProcessor, self).__init__(**traits)
resp_inc = "respiration" in self.physiodata.contents
z0_inc = "z0" in self.physiodata.contents
if z0_inc and resp_inc:
self.state = "z0_resp"
messagebox("Using both respiration belt and ICG")
z0_signal = self.physiodata.z0_data
dzdt_signal = self.physiodata.dzdt_data
resp_signal = self.physiodata.respiration_data
elif resp_inc and not z0_inc:
self.state = "resp"
messagebox("Only respiration belt data will be used.")
resp_signal = self.physiodata.resp_data
z0_signal = None
dzdt_signal = None
elif z0_inc and not resp_inc:
self.state = "z0"
messagebox("Using only z0 channel to estimate respiration")
resp_signal = self.physiodata.z0_data
z0_signal = self.physiodata.z0_data
dzdt_signal = self.physiodata.dzdt_data
self.resp_polort = 1
else:
self.state = "unusable"
messagebox("No respiration belt or z0 channels found")
# Establish the maximum shared length of resp_inhale_begin_values
signals = [sig for sig in (resp_signal, z0_signal,dzdt_signal) if \
sig is not None]
if len(signals) > 1:
minlen = min([len(sig) for sig in signals])
else:
minlen = len(signals[0])
# Establish a time array
if resp_inc:
self.time = TimeSeries(physiodata=self.physiodata,
contains="respiration").time[:minlen]
else:
self.time = TimeSeries(physiodata=self.physiodata,
contains="z0").time[:minlen]
# Get out the final signals
if z0_inc:
self.raw_resp_signal = z0_signal[:minlen].copy()
self.raw_resp_signal[:50] = self.raw_resp_signal.mean()
self.raw_z0_signal = z0_signal[:minlen].copy()
self.raw_z0_signal[:50] = self.raw_z0_signal.mean()
self.raw_dzdt_signal = dzdt_signal[:minlen].copy()
self.raw_dzdt_signal[:50] = self.raw_dzdt_signal.mean()
if resp_inc:
self.raw_resp_signal = resp_signal[:minlen].copy()
# if data already exists, it can't be dirty
if self.physiodata.resp_exhale_begin_times.size > 0: self.dirty = False
self.on_trait_change(self._parameter_changed,
"resp_polort,resp_high_freq_cutoff")
@cached_property
def _get_resp_signal(self):
resp_signal = winsorize(self.raw_resp_signal)
return (resp_signal - resp_signal.mean()) / resp_signal.std()
def _parameter_changed(self):
self.dirty = True
def _b_process_fired(self):
self.process()
def process(self):
"""
processes the respiration timeseries
"""
sampling_rate = 1. / (self.time[1] - self.time[0])
# Respiration belts can lose tension over time.
# This removes linear trends
if self.resp_polort > 0:
pfit = legendre_detrend(self.resp_signal, self.resp_polort)
if not pfit.shape == self.time.shape:
messagebox("Legendre detrend failed")
return
self.polyfilt_resp = pfit
else:
self.polyfilt_resp = self.resp_signal
lpd = lowpass(self.polyfilt_resp, self.resp_high_freq_cutoff,
sampling_rate)
if not lpd.shape == self.time.shape:
messagebox("lowpass filter failed")
return
self.lpfilt_resp = (lpd - lpd.mean()) / lpd.std()
resp_inhale_begin_indices, resp_exhale_begin_indices = find_peaks(
self.lpfilt_resp, maxima=True, minima=True)
self.resp_inhale_begin_times = self.time[resp_inhale_begin_indices]
self.resp_exhale_begin_times = self.time[resp_exhale_begin_indices]
self.resp_corrected_z0 = regress_out(self.raw_z0_signal,
self.lpfilt_resp)
self.resp_corrected_dzdt = regress_out(self.raw_dzdt_signal,
self.lpfilt_resp)
# update the scatterplot if we're interactive
if self.resp_plot_data is not None:
self.resp_plot_data.set_data("inhale_times",
self.resp_inhale_begin_times)
self.resp_plot_data.set_data(
"inhale_values", self.lpfilt_resp[resp_inhale_begin_indices])
self.resp_plot_data.set_data("exhale_times",
self.resp_exhale_begin_times)
self.resp_plot_data.set_data(
"exhale_values", self.lpfilt_resp[resp_exhale_begin_indices])
self.resp_plot_data.set_data("lpfilt_resp", self.lpfilt_resp)
self.dzdt_plot_data.set_data("cleaned_data",
self.resp_corrected_dzdt)
self.z0_plot_data.set_data("cleaned_data", self.resp_corrected_z0)
else:
print "plot data is none"
# Update the respiration cycles cached_pro
times = np.concatenate([
np.zeros(1), self.resp_exhale_begin_times,
self.resp_inhale_begin_times, self.time[-1, np.newaxis]
])
vals = np.concatenate([
np.zeros(1),
np.zeros_like(resp_exhale_begin_indices),
0.5 * np.ones_like(resp_inhale_begin_indices),
np.zeros(1)
])
srt = np.argsort(times)
terp = interp1d(times[srt], vals[srt])
self.respiration_cycle = terp(self.time)
self.respiration_amount = np.abs(
np.ediff1d(self.respiration_cycle, to_begin=0))
def _resp_plot_default(self):
# Create plotting components
self.resp_plot_data = ArrayPlotData(
time=self.time,
inhale_times=self.resp_inhale_begin_times,
inhale_values=self.resp_inhale_begin_values,
exhale_times=self.resp_exhale_begin_times,
exhale_values=self.resp_exhale_begin_values,
filtered_resp=self.resp_signal,
lpfilt_resp=self.lpfilt_resp)
plot = Plot(self.resp_plot_data)
plot.plot(("time", "filtered_resp"), color="blue", line_width=1)
plot.plot(("time", "lpfilt_resp"), color="green", line_width=1)
# Plot the inhalation peaks
plot.plot(("inhale_times", "inhale_values"),
type="scatter",
marker="square")
plot.plot(("exhale_times", "exhale_values"),
type="scatter",
marker="circle")
plot.title = "Respiration"
plot.title_position = "right"
plot.title_angle = 270
plot.padding = 20
return plot
def _z0_plot_default(self):
self.z0_plot_data = ArrayPlotData(time=self.time,
raw_data=self.raw_z0_signal,
cleaned_data=self.resp_corrected_z0)
plot = Plot(self.z0_plot_data)
plot.plot(("time", "raw_data"), color="blue", line_width=1)
plot.plot(("time", "cleaned_data"), color="green", line_width=1)
plot.title = "z0"
plot.title_position = "right"
plot.title_angle = 270
plot.padding = 20
return plot
def _dzdt_plot_default(self):
"""
Creates a plot of the ecg_ts data and the signals derived during
the Pan Tomkins algorithm
"""
# Create plotting components
self.dzdt_plot_data = ArrayPlotData(
time=self.time,
raw_data=self.raw_dzdt_signal,
cleaned_data=self.resp_corrected_dzdt)
plot = Plot(self.dzdt_plot_data)
plot.plot(("time", "raw_data"), color="blue", line_width=1)
plot.plot(("time", "cleaned_data"), color="green", line_width=1)
plot.title = "dZ/dt"
plot.title_position = "right"
plot.title_angle = 270
plot.padding = 20
return plot
def _plots_default(self):
plots_to_include = ()
if self.state in ("z0_resp", "z0"):
self.index_range = self.resp_plot.index_range
self.dzdt_plot.index_range = self.index_range
self.z0_plot.index_range = self.index_range
plots_to_include = [self.resp_plot, self.z0_plot, self.dzdt_plot]
elif self.state == "resp":
self.index_range = self.resp_plot.index_range
plots_to_include = [self.resp_plot]
return VPlotContainer(*plots_to_include)
@on_trait_change("window_size,start_time")
def update_plot_range(self):
self.resp_plot.index_range.high = self.start_time + self.window_size
self.resp_plot.index_range.low = self.start_time
proc_params_group = Group(Group(
Item("resp_polort"),
Item("resp_high_freq_cutoff"),
Item("b_process",
show_label=False,
enabled_when="state != unusable and dirty"),
label="Resp processing options",
show_border=True,
orientation="vertical",
springy=True),
orientation="horizontal")
plot_group = Group(
Group(Item("plots", editor=ComponentEditor(), width=800, height=700),
show_labels=False), Item("start_time"), Item("window_size"))
traits_view = MEAPView(
VSplit(
plot_group,
proc_params_group,
),
resizable=True,
win_title="Process Respiration Data",
)
class GroupRegisterDZDT(HasTraits):
physiodata = Instance(PhysioData)
global_ensemble = Instance(GlobalEnsembleAveragedHeartBeat)
srvf_lambda = DelegatesTo("physiodata")
srvf_max_karcher_iterations = DelegatesTo("physiodata")
srvf_update_min = DelegatesTo("physiodata")
srvf_karcher_mean_subset_size = DelegatesTo("physiodata")
dzdt_srvf_karcher_mean = DelegatesTo("physiodata")
dzdt_karcher_mean = DelegatesTo("physiodata")
dzdt_warping_functions = DelegatesTo("physiodata")
srvf_use_moving_ensembled = DelegatesTo("physiodata")
bspline_before_warping = DelegatesTo("physiodata")
dzdt_functions_to_warp = DelegatesTo("physiodata")
# Configures the slice of time to be registered
srvf_t_min = DelegatesTo("physiodata")
srvf_t_max = DelegatesTo("physiodata")
dzdt_karcher_mean_time = DelegatesTo("physiodata")
dzdt_mask = Array
# Holds indices of beats used to calculate initial Karcher mean
dzdt_karcher_mean_inputs = DelegatesTo("physiodata")
dzdt_karcher_mean_over_iterations = DelegatesTo("physiodata")
dzdt_num_inputs_to_group_warping = DelegatesTo("physiodata")
srvf_iteration_distances = DelegatesTo("physiodata")
srvf_iteration_energy = DelegatesTo("physiodata")
# For calculating multiple modes
all_beats_registered_to_initial = Bool(False)
all_beats_registered_to_mode = Bool(False)
n_modes = DelegatesTo("physiodata")
max_kmeans_iterations = DelegatesTo("physiodata")
mode_dzdt_karcher_means = DelegatesTo("physiodata")
mode_cluster_assignment = DelegatesTo("physiodata")
mode_dzdt_srvf_karcher_means = DelegatesTo("physiodata")
# graphics items
karcher_plot = Instance(Plot, transient=True)
registration_plot = Instance(HPlotContainer, transient=True)
karcher_plotdata = Instance(ArrayPlotData, transient=True)
# Buttons
b_calculate_karcher_mean = Button(label="Calculate Karcher Mean")
b_align_all_beats = Button(label="Warp all")
b_find_modes = Button(label="Discover Modes")
b_edit_modes = Button(label="Score Modes")
interactive = Bool(False)
# Holds the karcher modes
mode_beat_train = Instance(ModeKarcherBeatTrain)
edit_listening = Bool(False,
desc="If true, update_plots is called"
" when a beat gets hand labeled")
def __init__(self, **traits):
super(GroupRegisterDZDT, self).__init__(**traits)
# Set the initial path to whatever's in the physiodata file
logger.info("Initializing dZdt registration")
# Is there already a Karcher mean in the physiodata?
self.karcher_mean_calculated = self.dzdt_srvf_karcher_mean.size > 0 \
and self.dzdt_karcher_mean.size > 0
# Process dZdt data before srvf analysis
self._update_original_functions()
self.n_functions = self.dzdt_functions_to_warp.shape[0]
self.n_samples = self.dzdt_functions_to_warp.shape[1]
self._init_warps()
self.select_new_samples()
def _mode_beat_train_default(self):
logger.info("creating default mea_beat_train")
assert self.physiodata is not None
mkbt = ModeKarcherBeatTrain(physiodata=self.physiodata)
return mkbt
def _init_warps(self):
""" For loading warps from mea.mat """
if self.dzdt_warping_functions.shape[0] == \
self.dzdt_functions_to_warp.shape[0]:
self.all_beats_registered_to_mode = True
self._forward_warp_beats()
def _global_ensemble_default(self):
return GlobalEnsembleAveragedHeartBeat(physiodata=self.physiodata)
def _karcher_plot_default(self):
"""
Instead of defining these in __init__, only
construct the plots when a ui is requested
"""
self.interactive = True
unreg_mean = self.global_ensemble.dzdt_signal
# Temporarily fill in the karcher mean
if not self.karcher_mean_calculated:
karcher_mean = unreg_mean[self.dzdt_mask]
else:
karcher_mean = self.dzdt_karcher_mean
self.karcher_plotdata = ArrayPlotData(
time=self.global_ensemble.dzdt_time,
unregistered_mean=self.global_ensemble.dzdt_signal,
karcher_mean=karcher_mean,
karcher_time=self.dzdt_karcher_mean_time)
karcher_plot = Plot(self.karcher_plotdata)
karcher_plot.plot(("time", "unregistered_mean"),
line_width=1,
color="lightblue")
line_plot = karcher_plot.plot(("karcher_time", "karcher_mean"),
line_width=3,
color="blue")[0]
# Create an overlay tool
karcher_plot.datasources['karcher_time'].sort_order = "ascending"
return karcher_plot
def _registration_plot_default(self):
"""
Instead of defining these in __init__, only
construct the plots when a ui is requested
"""
unreg_mean = self.global_ensemble.dzdt_signal
# Temporarily fill in the karcher mean
if not self.karcher_mean_calculated:
karcher_mean = unreg_mean[self.dzdt_mask]
else:
karcher_mean = self.dzdt_karcher_mean
self.single_registration_plotdata = ArrayPlotData(
karcher_time=self.dzdt_karcher_mean_time,
karcher_mean=karcher_mean,
registered_func=karcher_mean)
self.single_plot = Plot(self.single_registration_plotdata)
self.single_plot.plot(("karcher_time", "karcher_mean"),
line_width=2,
color="blue")
self.single_plot.plot(("karcher_time", "registered_func"),
line_width=2,
color="maroon")
if self.all_beats_registered_to_initial or \
self.all_beats_registered_to_mode:
image_data = self.registered_functions.copy()
else:
image_data = self.dzdt_functions_to_warp.copy()
# Create a plot of all the functions registered or not
self.all_registration_plotdata = ArrayPlotData(image_data=image_data)
self.all_plot = Plot(self.all_registration_plotdata)
self.all_plot.img_plot("image_data", colormap=jet)
return HPlotContainer(self.single_plot, self.all_plot)
def _forward_warp_beats(self):
""" Create registered beats to plot, since they're not stored """
pass
logger.info("Applying warps to functions for plotting")
# Re-create gam
gam = self.dzdt_warping_functions - self.srvf_t_min
gam = gam / (self.srvf_t_max - self.srvf_t_min)
aligned_functions = np.zeros_like(self.dzdt_functions_to_warp)
t = self.dzdt_karcher_mean_time
for k in range(self.n_functions):
aligned_functions[k] = np.interp((t[-1] - t[0]) * gam[k] + t[0], t,
self.dzdt_functions_to_warp[k])
self.registered_functions = aligned_functions
@on_trait_change("dzdt_num_inputs_to_group_warping")
def select_new_samples(self):
nbeats = self.dzdt_functions_to_warp.shape[0]
nsamps = min(self.dzdt_num_inputs_to_group_warping, nbeats)
self.dzdt_karcher_mean_inputs = np.random.choice(nbeats,
size=nsamps,
replace=False)
@on_trait_change(
("physiodata.srvf_lambda, "
"physiodata.srvf_update_min, physiodata.srvf_use_moving_ensembled, "
"physiodata.srvf_karcher_mean_subset_size, "
"physiodata.bspline_before_warping"))
def params_edited(self):
self.dirty = True
self.karcher_mean_calculated = False
self.all_beats_registered_to_initial = False
self.all_beats_registered_to_mode = False
self._update_original_functions()
def _update_original_functions(self):
logger.info("updating time slice and functions to register")
# Get the time relative to R
dzdt_time = np.arange(self.physiodata.dzdt_matrix.shape[1],dtype=np.float) \
- self.physiodata.dzdt_pre_peak
self.dzdt_mask = (dzdt_time >= self.srvf_t_min) * (dzdt_time <=
self.srvf_t_max)
srvf_time = dzdt_time[self.dzdt_mask]
self.dzdt_karcher_mean_time = srvf_time
# Extract corresponding data
self.dzdt_functions_to_warp = self.physiodata.mea_dzdt_matrix[
: , self.dzdt_mask] if \
self.srvf_use_moving_ensembled else self.physiodata.dzdt_matrix[
: , self.dzdt_mask]
if self.bspline_before_warping:
logger.info("Smoothing inputs with B-Splines")
self.dzdt_functions_to_warp = np.row_stack([ UnivariateSpline(
self.dzdt_karcher_mean_time, func, s=0.05)(self.dzdt_karcher_mean_time) \
for func in self.dzdt_functions_to_warp]
)
if self.interactive:
self.all_registration_plotdata.set_data(
"image_data", self.dzdt_functions_to_warp.copy())
self.all_plot.request_redraw()
def _b_calculate_karcher_mean_fired(self):
self.calculate_karcher_mean()
def calculate_karcher_mean(self):
"""
Calculates an initial Karcher Mean.
"""
reg_prob = RegistrationProblem(
self.dzdt_functions_to_warp[self.dzdt_karcher_mean_inputs].T,
sample_times=self.dzdt_karcher_mean_time,
max_karcher_iterations=self.srvf_max_karcher_iterations,
lambda_value=self.srvf_lambda,
update_min=self.srvf_update_min)
reg_prob.run_registration_parallel()
reg_problem = reg_prob
self.dzdt_karcher_mean = reg_problem.function_karcher_mean
self.dzdt_srvf_karcher_mean = reg_problem.srvf_karcher_mean
self.karcher_mean_calculated = True
# Update plots if this is interactive
if self.interactive:
self.karcher_plotdata.set_data("karcher_mean",
self.dzdt_karcher_mean)
self.karcher_plot.request_redraw()
self.single_registration_plotdata.set_data("karcher_mean",
self.dzdt_karcher_mean)
self.single_plot.request_redraw()
self.rp = reg_problem
def _b_align_all_beats_fired(self):
self.align_all_beats_to_initial()
def _b_find_modes_fired(self):
self.detect_modes()
def detect_modes(self):
"""
Uses the SRD-based clustering method described in Kurtek 2017
"""
if not self.karcher_mean_calculated:
fail("Must calculate an initial Karcher mean first")
return
if not self.all_beats_registered_to_initial:
fail("All beats must be registered to the initial Karcher mean")
return
# Calculate the SRDs
dzdt_functions_to_warp = self.dzdt_functions_to_warp.T
warps = self.dzdt_warping_functions.T
wmax = warps.max()
wmin = warps.min()
warps = (warps - wmin) / (wmax - wmin)
densities = np.diff(warps, axis=0)
SRDs = np.sqrt(densities)
# pairwise distances
srd_pairwise = pairwise_distances(SRDs.T, metric=fisher_rao_dist)
tri = srd_pairwise[np.triu_indices_from(srd_pairwise, 1)]
linkage = complete(tri)
# Performs an iteration of k-means
def cluster_karcher_means(initial_assignments):
cluster_means = {}
cluster_ids = np.unique(initial_assignments).tolist()
warping_functions = np.zeros_like(SRDs)
# Calculate a Karcher mean for each cluster
for cluster_id in cluster_ids:
print "Cluster ID:", cluster_id
cluster_id_mask = initial_assignments == cluster_id
cluster_srds = SRDs[:, cluster_id_mask]
# If there is only a single SRD in this cluster, it is the mean
if cluster_id_mask.sum() == 1:
cluster_means[cluster_id] = cluster_srds
continue
# Run group registration to get Karcher mean
cluster_reg = RegistrationProblem(
cluster_srds,
sample_times=np.arange(SRDs.shape[0], dtype=np.float),
max_karcher_iterations=self.srvf_max_karcher_iterations,
lambda_value=self.srvf_lambda,
update_min=self.srvf_update_min)
cluster_reg.run_registration_parallel()
cluster_means[cluster_id] = cluster_reg.function_karcher_mean
warping_functions[:,
cluster_id_mask] = cluster_reg.mean_to_orig_warps
# Scale the cluster Karcher means so the FR distance works
scaled_cluster_means = {}
for k, v in cluster_means.iteritems():
scaled_cluster_means[k] = rescale_cluster_mean(v)
# There are now k cluster means, which is closest for each SRD?
# Also save its distance to its cluster's Karcher mean
srd_cluster_assignments, srd_cluster_distances = get_closest_mean(
SRDs, scaled_cluster_means)
return srd_cluster_assignments, srd_cluster_distances, scaled_cluster_means, warping_functions
# Iterate until assignments stabilize
last_assignments = fcluster(linkage,
self.n_modes,
criterion="maxclust")
stabilized = False
n_iters = 0
old_assignments = [last_assignments]
old_means = []
while not stabilized and n_iters < self.max_kmeans_iterations:
logger.info("Iteration %d", n_iters)
assignments, distances, cluster_means, warping_funcs = cluster_karcher_means(
last_assignments)
stabilized = np.all(last_assignments == assignments)
last_assignments = assignments.copy()
old_assignments.append(last_assignments)
old_means.append(cluster_means)
n_iters += 1
# Finalize the clusters by aligning all the functions to the cluster mean
# Iterate until assignments stabilize
cluster_means = {}
cluster_ids = np.unique(assignments)
warping_functions = np.zeros_like(dzdt_functions_to_warp)
self.registered_functions = np.zeros_like(self.dzdt_functions_to_warp)
# Calculate a Karcher mean for each cluster
for cluster_id in cluster_ids:
cluster_id_mask = assignments == cluster_id
cluster_funcs = self.dzdt_functions_to_warp.T[:, cluster_id_mask]
# If there is only a single SRD in this cluster, it is the mean
if cluster_id_mask.sum() == 1:
cluster_means[cluster_id] = cluster_funcs
continue
# Run group registration to get Karcher mean
cluster_reg = RegistrationProblem(
cluster_funcs,
sample_times=self.dzdt_karcher_mean_time,
max_karcher_iterations=self.srvf_max_karcher_iterations,
lambda_value=self.srvf_lambda,
update_min=self.srvf_update_min)
cluster_reg.run_registration_parallel()
cluster_means[cluster_id] = cluster_reg.function_karcher_mean
warping_functions[:,
cluster_id_mask] = cluster_reg.mean_to_orig_warps
self.registered_functions[
cluster_id_mask] = cluster_reg.registered_functions.T
# Save the warps to the modes as the final warping functions
self.dzdt_warping_functions = warping_functions.T \
* (self.srvf_t_max - self.srvf_t_min) \
+ self.srvf_t_min
# re-order the means
cluster_ids = sorted(cluster_means.keys())
final_assignments = np.zeros_like(assignments)
final_modes = []
for final_id, orig_id in enumerate(cluster_ids):
final_assignments[assignments == orig_id] = final_id
final_modes.append(cluster_means[orig_id].squeeze())
self.mode_dzdt_karcher_means = np.row_stack(final_modes)
self.mode_cluster_assignment = final_assignments
self.all_beats_registered_to_mode = True
def align_all_beats_to_initial(self):
if not self.karcher_mean_calculated:
logger.warn("Calculate Karcher mean first")
return
logger.info("Aligning all beats to the Karcher Mean")
if self.interactive:
progress = ProgressDialog(
title="ICG Warping",
min=0,
max=len(self.physiodata.peak_times),
show_time=True,
message="Warping dZ/dt to Karcher Mean...")
progress.open()
template_func = self.dzdt_srvf_karcher_mean
normed_template_func = template_func / np.linalg.norm(template_func)
fy, fx = np.gradient(self.dzdt_functions_to_warp.T, 1, 1)
srvf_functions = (fy / np.sqrt(np.abs(fy) + eps)).T
gam = np.zeros(self.dzdt_functions_to_warp.shape, dtype=np.float)
aligned_functions = self.dzdt_functions_to_warp.copy()
logger.info("aligned_functions %d", id(aligned_functions))
logger.info("self.dzdt_functions_to_warp %d",
id(self.dzdt_functions_to_warp))
t = self.dzdt_karcher_mean_time
for k in range(self.n_functions):
q_c = srvf_functions[k] / np.linalg.norm(srvf_functions[k])
G, T = dp(normed_template_func, t, q_c, t, t, t, self.srvf_lambda)
gam0 = np.interp(self.dzdt_karcher_mean_time, T, G)
gam[k] = (gam0 - gam0[0]) / (gam0[-1] - gam0[0]) # change scale
aligned_functions[k] = np.interp((t[-1] - t[0]) * gam[k] + t[0], t,
self.dzdt_functions_to_warp[k])
if self.interactive:
# Update the image plot
self.all_registration_plotdata.set_data(
"image_data", aligned_functions)
# Update the registration plot
self.single_registration_plotdata.set_data(
"registered_func", aligned_functions[k])
self.single_plot.request_redraw()
(cont, skip) = progress.update(k)
self.registered_functions = aligned_functions.copy()
self.dzdt_warping_functions = gam * (
self.srvf_t_max - self.srvf_t_min) + \
self.srvf_t_min
if self.interactive:
progress.update(k + 1)
self.all_beats_registered_to_initial = True
def _b_edit_modes_fired(self):
self.mode_beat_train.edit_traits()
def _point_plots_default(self):
"""
Instead of defining these in __init__, only
construct the plots when a ui is requested
"""
self.point_plotdata = ArrayPlotData(
peak_times=self.physiodata.peak_times.flatten(),
x_times=self.physiodata.x_indices - self.physiodata.dzdt_pre_peak,
lvet=self.physiodata.lvet,
pep=self.physiodata.pep)
container = VPlotContainer(resizable="hv",
bgcolor="lightgray",
fill_padding=True,
padding=10)
for sig in ("pep", "x_times", "lvet"):
temp_plt = Plot(self.point_plotdata)
temp_plt.plot(("peak_times", sig), line_width=2)
temp_plt.title = sig
container.add(temp_plt)
container.padding_top = 10
return container
mean_widgets = VGroup(VGroup(Item("karcher_plot",
editor=ComponentEditor(),
show_label=False),
Item("registration_plot",
editor=ComponentEditor(),
show_label=False),
show_labels=False),
Item("srvf_use_moving_ensembled",
label="Use Moving Ensembled dZ/dt"),
Item("bspline_before_warping",
label="B Spline smoothing"),
Item("srvf_t_min", label="Epoch Start Time"),
Item("srvf_t_max", label="Epoch End Time"),
Item("srvf_lambda", label="Lambda Value"),
Item("dzdt_num_inputs_to_group_warping",
label="Template uses N beats"),
Item("srvf_max_karcher_iterations",
label="Max Karcher Iterations"),
HGroup(
Item("b_calculate_karcher_mean",
label="Step 1:",
enabled_when="dirty"),
Item("b_align_all_beats",
label="Step 2:",
enabled_when="karcher_mean_calculated")),
label="Initial Karcher Mean")
mode_widgets = VGroup(
Item("n_modes", label="Number of Modes/Clusters"),
Item("max_kmeans_iterations"),
Item("b_find_modes",
show_label=False,
enabled_when="all_beats_registered_to_initial"),
Item("b_edit_modes",
show_label=False,
enabled_when="all_beats_registered_to_mode"))
traits_view = MEAPView(HSplit(mean_widgets, mode_widgets),
resizable=True,
win_title="ICG Warping Tools",
width=800,
height=700,
buttons=[OKButton, CancelButton])
class MEAPTimeseries(HasTraits):
physiodata = Instance(PhysioData)
plot = Instance(Plot, transient=True)
plotdata = Instance(ArrayPlotData, transient=True)
selection = Instance(BeatSelection, transient=True)
signal = Str
selected_beats = Array
index_datasourse = Instance(DataRange1D)
marker_size = Array
metadata_name = Str
selected = Event
selected_range = Tuple
traits_view = MEAPView(Group(Item('plot',
editor=ComponentEditor(size=size),
show_label=False),
orientation="vertical"),
resizable=True,
win_title=title)
def __init__(self, **traits):
super(MEAPTimeseries, self).__init__(**traits)
self.metadata_name = self.signal + "_selection"
def _selection_changed(self):
selection = self.selection.selection
logger.info("%s selection changed to %s", self.signal, str(selection))
if selection is None or len(selection) == 0:
return
self.selected_range = selection
self.selected = True
def _plot_default(self):
plot = Plot(self.plotdata)
if self.signal in ("tpr", "co", "sv"):
rc_signal = "resp_corrected_" + self.signal
if rc_signal in self.plotdata.arrays and self.plotdata.arrays[
rc_signal].size > 0:
# Plot the resp-uncorrected version underneath
plot.plot(("peak_times", self.signal),
type="line",
color="purple")
signal = rc_signal
signal = self.signal
elif self.signal == "hr":
plot.plot(("peak_times", self.signal), type="line", color="purple")
signal = "mea_hr"
else:
signal = self.signal
# Create the plot
plot.plot(("peak_times", signal), type="line", color="blue")
plot.plot(("peak_times", signal, "beat_type"),
type="cmap_scatter",
color_mapper=jet,
name="my_plot",
marker="circle",
border_visible=False,
outline_color="transparent",
bg_color="white",
index_sort="ascending",
marker_size=3,
fill_alpha=0.8)
# Tweak some of the plot properties
plot.title = self.signal #"Scatter Plot With Lasso Selection"
plot.title_position = "right"
plot.title_angle = 270
plot.line_width = 1
plot.padding = 20
# Right now, some of the tools are a little invasive, and we need the
# actual ScatterPlot object to give to them
my_plot = plot.plots["my_plot"][0]
# Attach some tools to the plot
self.selection = BeatSelection(component=my_plot)
my_plot.active_tool = self.selection
selection_overlay = RangeSelectionOverlay(component=my_plot)
my_plot.overlays.append(selection_overlay)
# Set up the trait handler for the selection
self.selection.on_trait_change(self._selection_changed,
'selection_completed')
return plot
class BatchFileTool(HasTraits):
# For saving outputs
file_suffix = Str("_finished.mea.mat")
input_file_extension = Enum(".mea.mat", ".acq", ".mat")
overwrite = Bool(False)
input_directory = Directory()
output_directory = Directory()
files = List(Instance(FileToProcess))
spreadsheet_file = File(exists=False)
b_save = Button("Save Spreadsheet")
def _input_file_extension_changed(self):
self._input_directory_changed()
def _input_directory_changed(self):
potential_files = glob(self.input_directory + "/*" +
self.input_file_extension)
potential_files = [f for f in potential_files if not \
f.endswith(self.file_suffix) ]
# Check if the output already exists
def make_output_file(input_file):
return input_file[:-len(self.input_file_extension
)] + self.file_suffix
self.files = [
FileToProcess(input_file = f, output_file=make_output_file(f)) \
for f in potential_files
]
# If no output directory is set, use the input directory
if self.output_directory == '':
self.output_directory = self.input_directory
def _b_save_fired(self):
def get_row():
return {
"file": "",
"outfile": "",
"weight": "",
"height_ft": "",
"weight": "",
"electrode_distance_front": "",
"electrode_distance_back": "",
"electrode_distance_left": "",
"electrode_distance_right": "",
"resp_max": "",
"resp_min": "",
"in_mri": "",
"control_base_impedance": ""
}
rows = []
for f in self.files:
row = get_row()
row['file'] = f.input_file
row['outfile'] = f.output_file
rows.append(row)
df = pd.DataFrame(rows)
logger.info("Writing spreadsheet to %s", self.spreadsheet_file)
df.to_excel(self.spreadsheet_file, index=False)
mean_widgets = VGroup(Item("input_file_extension"),
Item("input_directory"), Item("output_directory"),
Item("file_suffix"), Item("spreadsheet_file"),
Item("b_save", show_label=False))
traits_view = MEAPView(HSplit(
Item("files", editor=files_table, show_label=False), mean_widgets),
resizable=True,
win_title="Create Batch Spreadsheet",
width=800,
height=700,
buttons=[OKButton, CancelButton])
class BatchGroupRegisterDZDT(HasTraits):
# Dummy physiodata to get defaults
physiodata = Instance(PhysioData)
# Parameters for SRVF registration
srvf_lambda = DelegatesTo("physiodata")
srvf_max_karcher_iterations = DelegatesTo("physiodata")
srvf_update_min = DelegatesTo("physiodata")
srvf_karcher_mean_subset_size = DelegatesTo("physiodata")
srvf_use_moving_ensembled = DelegatesTo("physiodata")
bspline_before_warping = DelegatesTo("physiodata")
dzdt_num_inputs_to_group_warping = DelegatesTo("physiodata")
srvf_t_min = DelegatesTo("physiodata")
srvf_t_max = DelegatesTo("physiodata")
n_modes = DelegatesTo("physiodata")
# For saving outputs
num_cores = Int(1)
file_suffix = Str()
overwrite = Bool(False)
input_directory = Directory()
output_directory = Directory()
files = List(Instance(FileToProcess))
b_run = Button(label="Run")
def __init__(self, **traits):
super(BatchGroupRegisterDZDT, self).__init__(**traits)
self.num_cores = multiprocessing.cpu_count()
def _physiodata_default(self):
return PhysioData()
@on_trait_change(("physiodata.srvf_karcher_iterations, "
"physiodata.srvf_use_moving_ensembled, "
"physiodata.srvf_karcher_mean_subset_size, "
"physiodata.bspline_before_warping"))
def params_edited(self):
self._input_directory_changed()
def _num_cores_changed(self):
num_cores = multiprocessing.cpu_count()
if self.num_cores < 1 or self.num_cores > num_cores:
self.num_cores = multiprocessing.cpu_count()
def _configure_io(self):
potential_files = glob(self.input_directory + "/*mea.mat")
potential_files = [f for f in potential_files if not \
f.endswith("_aligned.mea.mat") ]
# Check if the output already exists
def make_output_file(input_file):
suffix = os.path.split(os.path.abspath(input_file))[1]
suffix = suffix[:-len(".mea.mat")] + self.file_suffix
return self.output_directory + "/" + suffix
self.files = [
FileToProcess(input_file = f, output_file=make_output_file(f)) \
for f in potential_files
]
def _output_directory_changed(self):
self._configure_io()
def _file_suffix_changed(self):
self._configure_io()
def _input_directory_changed(self):
self._configure_io()
def _b_run_fired(self):
files_to_run = [f for f in self.files if not f.finished]
logger.info("Processing %d files using %d cpus", len(files_to_run),
self.num_cores)
pool = multiprocessing.Pool(self.num_cores)
arglist = [
(f.input_file, f.output_file, self.srvf_lambda,
self.srvf_max_karcher_iterations, self.srvf_update_min,
self.srvf_karcher_mean_subset_size,
self.srvf_use_moving_ensembled, self.bspline_before_warping,
self.dzdt_num_inputs_to_group_warping, self.srvf_t_min,
self.srvf_t_max, self.n_modes) for f in files_to_run
]
pool.map(process_physio_file, arglist)
mean_widgets = VGroup(
Item("input_directory"), Item("output_directory"), Item("file_suffix"),
Item("srvf_use_moving_ensembled", label="Use Moving Ensembled dZ/dt"),
Item("bspline_before_warping", label="B Spline smoothing"),
Item("srvf_lambda", label="Lambda Value"),
Item("dzdt_num_inputs_to_group_warping",
label="Template uses N beats"),
Item("srvf_max_karcher_iterations", label="Max Iterations"),
Item("n_modes"), Item("srvf_t_min"), Item("srvf_t_max"),
Item("num_cores"), Item("b_run", show_label=False))
traits_view = MEAPView(HSplit(
Item("files", editor=files_table, show_label=False), mean_widgets),
resizable=True,
win_title="Batch Warp dZ/dt",
width=800,
height=700,
buttons=[OKButton, CancelButton])
class MEAPPipeline(HasTraits):
physiodata = Instance(PhysioData)
file = File
outfile = File
mapping_txt = File
importer = Instance(Importer)
importer_kwargs = Dict
b_import = Button(label="Import data")
b_subject_info = Button(label="Subject Info")
b_inspect = Button(label="Inspect data")
b_resp = Button(label="Process Resp")
b_detect = Button(label="Detect QRS Complexes")
b_custom_points = Button(label="Label Waveform Points")
b_moving_ens = Button(label="Compute Moving Ensembles")
b_register = Button(label="Register dZ/dt")
b_fmri_tool = Button(label="Process fMRI")
b_load_experiment = Button(label="Load Design File")
b_save = Button(label="save .meap file")
b_clear_mem = Button(label="Clear Memory")
interactive = Bool(False)
saved = Bool(False)
peaks_detected = Bool(False)
global_ensemble_marked = Bool(False)
def _b_clear_mem_fired(self):
self.physiodata = None
self.global_ensemble_marked = False
self.peaks_detected = False
def import_data(self):
logger.info("Loading %s", self.file)
for k, v in self.importer_kwargs.iteritems():
logger.info("Using attr '%s' from excel file", k)
if not os.path.exists(self.file):
fail("unable to open file %s" % self.file,
interactive=self.interactive)
return
elif self.file.endswith(".acq"):
importer = AcqImporter(path=str(self.file),
mapping_txt=self.mapping_txt,
**self.importer_kwargs)
elif self.file.endswith(".mea.mat"):
pd = load_from_disk(self.file)
self.physiodata = pd
if self.physiodata.using_hand_marked_point_priors:
self.global_ensemble_marked = True
if self.physiodata.peak_indices.size > 0:
self.peaks_detected = True
return
elif self.file.endswith(".mat"):
importer = MatfileImporter(path=str(self.file),
**self.importer_kwargs)
else:
return
ui = importer.edit_traits(kind="livemodal")
if not ui.result:
logger.info("Import cancelled")
return
self.physiodata = importer.get_physiodata()
def _b_import_fired(self):
self.import_data()
def _b_resp_fired(self):
RespirationProcessor(physiodata=self.physiodata).edit_traits(
kind="livemodal")
def _b_subject_info_fired(self):
SubjectInfo(physiodata=self.physiodata).edit_traits(kind="livemodal")
def _b_custom_points_fired(self):
ge = GlobalEnsembleAveragedHeartBeat(physiodata=self.physiodata)
if not self.physiodata.using_hand_marked_point_priors:
ge.mark_points()
ge.edit_traits(kind="livemodal")
self.physiodata.using_hand_marked_point_priors = True
self.global_ensemble_marked = True
def _b_inspect_fired(self):
DataPlot(physiodata=self.physiodata).edit_traits()
def _b_detect_fired(self):
detector = PanTomkinsDetector(physiodata=self.physiodata)
ui = detector.edit_traits(kind="livemodal")
if ui.result:
self.peaks_detected = True
def _b_moving_ens_fired(self):
MovingEnsembler(physiodata=self.physiodata).edit_traits()
def _b_register_fired(self):
GroupRegisterDZDT(physiodata=self.physiodata).edit_traits()
def _b_save_fired(self):
print "writing", self.outfile
if os.path.exists(self.outfile):
logger.warn("%s already exists", self.outfile)
self.physiodata.save(self.outfile)
self.saved = True
logger.info("saved %s", self.outfile)
def _b_fmri_tool_fired(self):
FMRITool(physiodata=self.physiodata).edit_traits()
traits_view = MEAPView(
VGroup(
VGroup(Item("file"), Item("outfile")),
VGroup(
spring,
Item("b_import",
show_label=False,
enabled_when=
"file.endswith('.acq') or file.endswith('.mat')"),
Item("b_inspect", enabled_when="physiodata is not None"),
Item("b_subject_info", enabled_when="physiodata is not None"),
Item("b_resp", enabled_when="physiodata is not None"),
Item("b_detect", enabled_when="physiodata is not None"),
Item("b_custom_points", enabled_when="peaks_detected"),
Item("b_moving_ens", enabled_when="global_ensemble_marked"),
Item("b_register", enabled_when="peaks_detected"),
Item("b_fmri_tool",
enabled_when=
"physiodata.processed_respiration_data.size > 0"),
Item("b_save",
enabled_when=
"outfile.endswith('.mea') or outfile.endswith('.mea.mat')"
),
Item("b_clear_mem"),
spring,
show_labels=False)))
class PanTomkinsDetector(HasTraits):
# Holds the data Source
physiodata = Instance(PhysioData)
ecg_ts = Instance(TimeSeries)
dirty = Bool(False)
# For visualization
plot = Instance(Plot, transient=True)
plot_data = Instance(ArrayPlotData, transient=True)
image_plot = Instance(Plot, transient=True)
image_plot_data = Instance(ArrayPlotData, transient=True)
image_selection_tool = Instance(ImageRangeSelector)
image_plot_selected = DelegatesTo("image_selection_tool")
peak_vis = Instance(ScatterPlot, transient=True)
scatter = Instance(ScatterPlot, transient=True)
start_time = Range(low=0, high=100000.0, initial=0.0)
window_size = Range(low=1.0, high=100000.0, initial=30.0)
peak_editor = Instance(PeakPickingTool, transient=True)
show_censor_regions = Bool(True)
# parameters for processing the raw data before PT detecting
bandpass_min = DelegatesTo("physiodata")
bandpass_max = DelegatesTo("physiodata")
smoothing_window_len = DelegatesTo("physiodata")
smoothing_window = DelegatesTo("physiodata")
pt_adjust = DelegatesTo("physiodata")
peak_threshold = DelegatesTo("physiodata")
apply_filter = DelegatesTo("physiodata")
apply_diff_sq = DelegatesTo("physiodata")
apply_smooth_ma = DelegatesTo("physiodata")
peak_window = DelegatesTo("physiodata")
qrs_source_signal = DelegatesTo("physiodata")
qrs_power_signal = Property(Array,
depends_on=qrs_power_signal_dependencies)
# Use a secondary signal to limit the search range
use_secondary_heartbeat = DelegatesTo("physiodata")
secondary_heartbeat = DelegatesTo("physiodata")
secondary_heartbeat_abs = DelegatesTo("physiodata")
secondary_heartbeat_pre_msec = DelegatesTo("physiodata")
secondary_heartbeat_window = DelegatesTo("physiodata")
secondary_heartbeat_window_len = DelegatesTo("physiodata")
secondary_heartbeat_n_likelihood_bins = DelegatesTo("physiodata")
aux_signal = Property(Array) #, depends_on=aux_signal_dependencies)
# Secondary ECG signal
can_use_ecg2 = Bool(False)
use_ECG2 = DelegatesTo("physiodata")
ecg2_weight = DelegatesTo("physiodata")
# The results of the peak search
peak_indices = DelegatesTo("physiodata")
peak_times = DelegatesTo("physiodata")
peak_values = Array
dne_peak_indices = DelegatesTo("physiodata")
dne_peak_times = DelegatesTo("physiodata")
dne_peak_values = Array
# Holds the timeseries for the signal vs noise thresholds
thr_times = Array
thr_vals = Array
# for pulling out data for aggregating ecg_ts, dzdt_ts and bp beats
ecg_matrix = DelegatesTo("physiodata")
# UI elements
b_detect = Button(label="Detect QRS", transient=True)
b_shape = Button(label="Shape-Based Tuning", transient=True)
def __init__(self, **traits):
super(PanTomkinsDetector, self).__init__(**traits)
self.ecg_ts = TimeSeries(physiodata=self.physiodata, contains="ecg")
# relevant data to be plotted
self.ecg_time = self.ecg_ts.time
self.can_use_ecg2 = "ecg2" in self.physiodata.contents
# Which ECG signal to use?
if self.qrs_source_signal == "ecg" or not self.can_use_ecg2:
self.ecg_signal = normalize(self.ecg_ts.data)
if self.can_use_ecg2:
self.ecg2_signal = normalize(self.physiodata.ecg2_data)
else:
self.ecg2_signal = None
else:
self.ecg_signal = normalize(self.physiodata.ecg2_data)
self.ecg2_signal = normalize(self.physiodata.ecg_data)
self.thr_times = self.ecg_time[np.array([0, -1])]
self.censored_intervals = self.physiodata.censored_intervals
# graphics containers
self.aux_window_graphics = []
self.censored_region_graphics = []
# If peaks are already available in the mea.mat,
# they have already been marked
if len(self.peak_times):
self.dirty = False
self.peak_values = self.ecg_signal[self.peak_indices]
if self.dne_peak_indices is not None and len(self.dne_peak_indices):
self.dne_peak_values = self.ecg_signal[self.dne_peak_indices]
def _b_shape_fired(self):
self.shape_based_tuning()
def shape_based_tuning(self):
logger.info("Running shape-based tuning")
qrs_stack = peak_stack(self.peak_indices,
self.qrs_power_signal,
pre_msec=300,
post_msec=700,
sampling_rate=self.physiodata.ecg_sampling_rate)
def _b_detect_fired(self):
self.detect()
def _show_censor_regions_changed(self):
for crg in self.censored_region_graphics:
crg.visible = self.show_censor_regions
self.plot.request_redraw()
@cached_property
def _get_qrs_power_signal(self):
if self.apply_filter:
filtered_ecg = normalize(
bandpass(self.ecg_signal, self.bandpass_min, self.bandpass_max,
self.ecg_ts.sampling_rate))
else:
filtered_ecg = self.ecg_signal
# Differentiate and square the signal?
if self.apply_diff_sq:
# Differentiate the signal and square it
diff_sq = np.ediff1d(filtered_ecg, to_begin=0)**2
else:
diff_sq = filtered_ecg
# If we're to apply a Moving Average smoothing
if self.apply_smooth_ma:
# MA smoothing
smooth_ma = smooth(diff_sq,
window_len=self.smoothing_window_len,
window=self.smoothing_window)
else:
smooth_ma = diff_sq
if not self.use_ECG2:
# for visualization purposes
return normalize(smooth_ma)
logger.info("Using 2nd ECG signal")
# Use secondary ECG signal and combine QRS power
if self.apply_filter:
filtered_ecg2 = normalize(
bandpass(self.ecg2_signal, self.bandpass_min,
self.bandpass_max, self.ecg_ts.sampling_rate))
else:
filtered_ecg2 = self.ecg2_signal
if self.apply_diff_sq:
diff_sq2 = np.ediff1d(filtered_ecg2, to_begin=0)**2
else:
diff_sq2 = filtered_ecg2
if self.apply_smooth_ma:
smooth_ma2 = smooth(diff_sq2,
window_len=self.smoothing_window_len,
window=self.smoothing_window)
else:
smooth_ma2 = diff_sq2
return normalize(((1 - self.ecg2_weight) * smooth_ma +
self.ecg2_weight * smooth_ma2)**2)
def _get_aux_signal(self):
if not self.use_secondary_heartbeat: return np.array([])
sig = getattr(self.physiodata, self.secondary_heartbeat + "_data")
if self.secondary_heartbeat_abs:
sig = np.abs(sig)
if self.secondary_heartbeat_window_len > 0:
sig = smooth(sig,
window_len=self.secondary_heartbeat_window_len,
window=self.secondary_heartbeat_window)
return normalize(sig)
@on_trait_change(algorithm_parameters)
def params_edited(self):
self.dirty = True
def update_aux_window_graphics(self):
if not hasattr(self, "ecg_trace") or not self.use_secondary_heartbeat:
return
#remove the old graphics
for aux_window in self.aux_window_graphics:
del self.ecg_trace.index.metadata[aux_window.metadata_name]
self.ecg_trace.overlays.remove(aux_window)
# add the new graphics
for n, (start, end) in enumerate(self.aux_windows / 1000.):
window_key = "aux%03d" % n
self.aux_window_graphics.append(
AuxSignalWindow(component=self.aux_trace,
metadata_name=window_key))
self.ecg_trace.overlays.append(self.aux_window_graphics[-1])
self.ecg_trace.index.metadata[window_key] = start, end
def get_aux_windows(self):
aux_peaks = find_peaks(self.aux_signal)
aux_pre_peak = aux_peaks - self.secondary_heartbeat_pre_msec
aux_windows = np.column_stack([aux_pre_peak, aux_peaks])
return aux_windows
def detect(self):
"""
Implementation of the Pan Tomkins QRS detector
"""
logger.info("Beginning QRS Detection")
t0 = time.time()
# The original paper used a different method for finding peaks
smoothdiff = normalize(np.ediff1d(self.qrs_power_signal, to_begin=0))
peaks = find_peaks(smoothdiff)
peak_amps = self.qrs_power_signal[peaks]
# Part 2: getting rid of useless peaks
# ====================================
# There are lots of small, irrelevant peaks that need to
# be discarded.
# 2a) remove peaks occurring in censored intervals
censor_peak_mask = censor_peak_times(
self.ecg_ts.
censored_regions, #TODO: switch to physiodata.censored_intervals
self.ecg_time[peaks])
n_removed_peaks = peaks.shape[0] - censor_peak_mask.sum()
logger.info("%d/%d potential peaks outside %d censored intervals",
n_removed_peaks, peaks.shape[0],
len(self.ecg_ts.censored_regions))
peaks = peaks[censor_peak_mask]
peak_amps = peak_amps[censor_peak_mask]
# 2b) if a second signal is used, make sure the ecg peaks are
# near aux signal peaks
if self.use_secondary_heartbeat:
self.aux_windows = self.get_aux_windows()
aux_mask = times_contained_in(peaks, self.aux_windows)
logger.info("Using secondary signal")
logger.info("%d aux peaks detected", self.aux_windows.shape[0])
logger.info("%d/%d peaks contained in second signal window",
aux_mask.sum(), peaks.shape[0])
peaks = peaks[aux_mask]
peak_amps = peak_amps[aux_mask]
# 2c) use otsu's method to find a cutoff value
peak_amp_thr = threshold_otsu(peak_amps) + self.pt_adjust
otsu_mask = peak_amps > peak_amp_thr
logger.info("otsu threshold: %.7f", peak_amp_thr)
logger.info("%d/%d peaks survive", otsu_mask.sum(), peaks.shape[0])
peaks = peaks[otsu_mask]
peak_amps = peak_amps[otsu_mask]
# 3) Make sure there is only one peak in each secondary window
# this is accomplished by estimating the distribution of peak
# times relative to aux window starts
if self.use_secondary_heartbeat:
npeaks = peaks.shape[0]
# obtain a distribution of times and amplitudes
rel_peak_times = np.zeros_like(peaks)
window_subsets = []
for start, end in self.aux_windows:
mask = np.flatnonzero((peaks >= start) & (peaks <= end))
if len(mask) == 0: continue
window_subsets.append(mask)
rel_peak_times[mask] = peaks[mask] - start
# how common are relative peak times relative to window starts
densities, bins = np.histogram(
rel_peak_times,
range=(0, self.secondary_heartbeat_pre_msec),
bins=self.secondary_heartbeat_n_likelihood_bins,
density=True)
likelihoods = densities[np.clip(
np.digitize(rel_peak_times, bins) - 1, 0,
self.secondary_heartbeat_n_likelihood_bins - 1)]
_peaks = []
# Pull out the maximal peak
for subset in window_subsets:
# If there's only a single peak contained, no need for math
if len(subset) == 1:
_peaks.append(peaks[subset[0]])
continue
_peaks.append(peaks[subset[np.argmax(likelihoods[subset])]])
peaks = np.array(_peaks)
logger.info("Only 1 peak per aux window allowed:" + \
" %d/%d peaks remaining",peaks.shape[0],npeaks)
# Check that no two peaks are too close:
peak_diffs = np.ediff1d(peaks, to_begin=500)
peaks = peaks[peak_diffs > 200] # Cutoff is 300BPM
# Stack the peaks and see if the original data has a higher value
raw_stack = peak_stack(peaks,
self.ecg_signal,
pre_msec=self.peak_window,
post_msec=self.peak_window,
sampling_rate=self.ecg_ts.sampling_rate)
adj_factors = np.argmax(raw_stack, axis=1) - self.peak_window
peaks = peaks + adj_factors
self.peak_indices = peaks
self.peak_values = self.ecg_signal[peaks]
self.peak_times = self.ecg_time[peaks]
self.thr_vals = np.array([peak_amp_thr] * 2)
t1 = time.time()
# update the scatterplot if we're interactive
if self.plot_data is not None:
self.plot_data.set_data("peak_times", self.peak_times)
self.plot_data.set_data("peak_values", self.peak_values)
self.plot_data.set_data("qrs_power", self.qrs_power_signal)
self.plot_data.set_data("aux_signal", self.aux_signal)
self.plot_data.set_data("thr_vals", self.thr_vals)
self.plot_data.set_data("thr_times", self.thr_vals)
self.plot_data.set_data(
"thr_times", np.array([self.ecg_time[0], self.ecg_time[-1]])),
self.update_aux_window_graphics()
self.plot.request_redraw()
self.image_plot_data.set_data("imagedata", self.ecg_matrix)
self.image_plot.request_redraw()
else:
print "plot data is none"
logger.info("found %d QRS complexes in %.3f seconds",
len(self.peak_indices), t1 - t0)
self.dirty = False
def _plot_default(self):
"""
Creates a plot of the ecg_ts data and the signals derived during
the Pan Tomkins algorithm
"""
# Create plotting components
self.plot_data = ArrayPlotData(
time=self.ecg_time,
raw_ecg=self.ecg_signal,
qrs_power=self.qrs_power_signal,
aux_signal=self.aux_signal,
# Ensembleable peaks
peak_times=self.peak_times,
peak_values=self.peak_values,
# Non-ensembleable, useful for HR, HRV
dne_peak_times=self.dne_peak_times,
dne_peak_values=self.dne_peak_values,
# Threshold slider bar
thr_times=np.array([self.ecg_time[0], self.ecg_time[-1]]),
thr_vals=np.array([0, 0]))
plot = Plot(self.plot_data, use_backbuffer=True)
self.aux_trace = plot.plot(("time", "aux_signal"),
color="purple",
alpha=0.6,
line_width=2)[0]
self.qrs_power_trace = plot.plot(("time", "qrs_power"),
color="blue",
alpha=0.8)[0]
self.ecg_trace = plot.plot(("time", "raw_ecg"),
color="red",
line_width=2)[0]
# Load the censor regions and add them to the plot
for n, (start, end) in enumerate(self.censored_intervals):
censor_key = "censor%03d" % n
self.censored_region_graphics.append(
StaticCensoredInterval(component=self.qrs_power_trace,
metadata_name=censor_key))
self.ecg_trace.overlays.append(self.censored_region_graphics[-1])
self.ecg_trace.index.metadata[censor_key] = start, end
# Line showing
self.threshold_trace = plot.plot(("thr_times", "thr_vals"),
color="black",
line_width=3)[0]
# Plot for plausible peaks
self.ppeak_vis = plot.plot(("dne_peak_times", "dne_peak_values"),
type="scatter",
marker="diamond")[0]
# Make a scatter plot where you can edit the peaks
self.peak_vis = plot.plot(("peak_times", "peak_values"),
type="scatter")[0]
self.scatter = plot.components[-1]
self.peak_editor = PeakPickingTool(self.scatter)
self.scatter.tools.append(self.peak_editor)
# when the user adds or removes a point, automatically extract
self.on_trait_event(self._change_peaks, "peak_editor.done_selecting")
self.scatter.overlays.append(
PeakPickingOverlay(component=self.scatter))
return plot
# TODO: have this update other variables in physiodata: hand_labeled, mea, etc
def _delete_peaks(self, peaks_to_delete):
pass
def _add_peaks(self, peaks_to_add):
pass
# End TODO
def _change_peaks(self):
if self.dirty:
messagebox("You shouldn't edit peaks until you've run Detect QRS")
interval = self.peak_editor.selection
if interval is None: return
mode = self.peak_editor.selection_purpose
logger.info("PeakPickingTool entered %s mode over %s", mode,
str(interval))
if mode == "delete":
# Do it for real peaks
ok_peaks = np.logical_not(
np.logical_and(self.peak_times > interval[0],
self.peak_times < interval[1]))
self.peak_indices = self.peak_indices[ok_peaks]
self.peak_values = self.peak_values[ok_peaks]
self.peak_times = self.peak_times[ok_peaks]
# And do it for
ok_dne_peaks = np.logical_not(
np.logical_and(self.dne_peak_times > interval[0],
self.dne_peak_times < interval[1]))
self.dne_peak_indices = self.dne_peak_indices[ok_dne_peaks]
self.dne_peak_values = self.dne_peak_values[ok_dne_peaks]
self.dne_peak_times = self.dne_peak_times[ok_dne_peaks]
else:
# Find the signal contained in the selection
sig = np.logical_and(self.ecg_time > interval[0],
self.ecg_time < interval[1])
sig_inds = np.flatnonzero(sig)
selected_sig = self.ecg_signal[sig_inds]
# find the peak in the selected region
peak_ind = sig_inds[0] + np.argmax(selected_sig)
# If we're in add peak mode, always make sure
# that only unique peaks get added:
if mode == "add":
real_peaks = np.sort(
np.unique(self.peak_indices.tolist() + [peak_ind]))
self.peak_indices = real_peaks
self.peak_values = self.ecg_signal[real_peaks]
self.peak_times = self.ecg_time[real_peaks]
else:
real_dne_peaks = np.sort(
np.unique(self.dne_peak_indices.tolist() + [peak_ind]))
self.dne_peak_indices = real_dne_peaks
self.dne_peak_values = self.ecg_signal[real_dne_peaks]
self.dne_peak_times = self.ecg_time[real_dne_peaks]
# update the scatterplot if we're interactive
if not self.plot_data is None:
self.plot_data.set_data("peak_times", self.peak_times)
self.plot_data.set_data("peak_values", self.peak_values)
self.plot_data.set_data("dne_peak_times", self.dne_peak_times)
self.plot_data.set_data("dne_peak_values", self.dne_peak_values)
self.image_plot_data.set_data("imagedata", self.ecg_matrix)
self.image_plot.request_redraw()
@on_trait_change("window_size,start_time")
def update_plot_range(self):
self.plot.index_range.high = self.start_time + self.window_size
self.plot.index_range.low = self.start_time
@on_trait_change("image_plot_selected")
def snap_to_image_selection(self):
if not self.peak_times.size > 0: return
tmin = self.peak_times[int(self.image_selection_tool.ymin)] - 2.
tmax = self.peak_times[int(self.image_selection_tool.ymax)] + 2.
logger.info("selection tool sends data to (%.2f, %.2f)", tmin, tmax)
self.plot.index_range.low = tmin - 2.
self.plot.index_range.high = tmax + 2.
def _image_plot_default(self):
# for image plot
img = self.ecg_matrix
if self.ecg_matrix.size == 0:
img = np.zeros((100, 100))
self.image_plot_data = ArrayPlotData(imagedata=img)
plot = Plot(self.image_plot_data)
self.image_selection_tool = ImageRangeSelector(component=plot,
tool_mode="range",
axis="value",
always_on=True)
plot.img_plot("imagedata",
colormap=jet,
name="plot1",
origin="bottom left")[0]
plot.overlays.append(self.image_selection_tool)
return plot
detection_params_group = VGroup(
HGroup(
Group(
VGroup(Item("use_secondary_heartbeat"),
Item("peak_window"),
Item("apply_filter"),
Item("bandpass_min"),
Item("bandpass_max"),
Item("smoothing_window_len"),
Item("smoothing_window"),
Item("pt_adjust"),
Item("apply_diff_sq"),
label="Pan Tomkins"),
VGroup( # Items for MultiSignal detection
Item("secondary_heartbeat"),
Item("secondary_heartbeat_pre_msec"),
Item("secondary_heartbeat_abs"),
Item("secondary_heartbeat_window"),
Item("secondary_heartbeat_window_len"),
label="MultiSignal Detection",
enabled_when="use_secondary_heartbeat"),
VGroup( # Items for two ECG Signals
Item("use_ECG2"),
Item("ecg2_weight"),
label="Multiple ECG",
enabled_when="can_use_ecg2"),
label="Beat Detection Options",
layout="tabbed",
show_border=True,
springy=True),
Item("image_plot", editor=ComponentEditor(), width=300),
show_labels=False),
Item("b_detect", enabled_when="dirty"),
Item("b_shape"),
show_labels=False)
plot_group = Group(
Group(Item("plot", editor=ComponentEditor(), width=800),
show_labels=False), Item("start_time"), Item("window_size"))
traits_view = MEAPView(
VSplit(
plot_group,
detection_params_group,
#orientation="vertical"
),
resizable=True,
buttons=[OKButton, CancelButton],
title="Detect Heart Beats")
class Importer(HasTraits):
path = File
channels = List(Instance(Channel))
mapping_txt = File()
mapper = Dict()
# --- Subject information
subject_age = CFloat(20.)
subject_gender = Enum("M","F")
subject_weight = CFloat(135.,label="Weight (lbs)")
subject_height_ft = CInt(5,label="Height (ft)",
desc="Subject's height in feet")
subject_height_in = CInt(10,label = "Height (in)",
desc="Subject's height in inches")
subject_electrode_distance_front = CFloat(32,
label="Impedance electrode distance (front)")
subject_electrode_distance_back = CFloat(32,
label="Impedance electrode distance (back)")
subject_electrode_distance_right = CFloat(32,
label="Impedance electrode distance (right)")
subject_electrode_distance_left = CFloat(32,
label="Impedance electrode distance (left)")
subject_in_mri = CBool(False)
subject_control_base_impedance = CFloat(0.,label="Control Imprdance",
desc="If in MRI, store the z0 value from outside the MRI")
subject_resp_max = CFloat(100.,label="Respiration circumference max (cm)")
subject_resp_min = CFloat(0.,label="Respiration circumference min (cm)")
def _channel_map_default(self):
return ChannelMapper()
def _mapping_txt_changed(self):
if not os.path.exists(self.mapping_txt): return
with open(self.mapping_txt) as f:
lines = [l.strip() for l in f]
self.mapper = {}
for line in lines:
strip = line.split("->")
if not len(strip) == 2:
logger.info("Unable to parse line: %s", line)
continue
map_from, map_to = [l.strip() for l in strip]
if map_to in SUPPORTED_SIGNALS:
self.mapper[map_from] = map_to
logger.info("mapping %s to %s",map_from,map_to)
else:
logger.info("Unrecognized channel: %s", map_to)
traits_view = MEAPView(
Group(
Item("channels", editor=channel_table),
label="Specify channel contents",
show_border=True,
show_labels=False
),
Group(
Item("subject_age"), Item("subject_gender"),
Item("subject_height_ft"), Item("subject_height_in"),
Item("subject_weight"),
Item("subject_electrode_distance_front"),
Item("subject_electrode_distance_back"),
Item("subject_electrode_distance_left"),
Item("subject_electrode_distance_right"),
Item("subject_resp_max"),Item("subject_resp_min"),
Item("subject_in_mri"),Item('subject_control_base_impedance'),
label="Participant Measurements"
),
buttons=[OKButton, CancelButton],
resizable=True,
win_title="Import Data",
)
def guess_channel_contents(self):
mapped = set([v for k,v in self.mapper.iteritems()])
for chan in self.channels:
if chan.name in self.mapper:
chan.contains = self.mapper[chan.name]
continue
cname = chan.name.lower()
if "magnitude" in cname and not "z0" in mapped:
chan.contains = "z0"
elif "ecg" in cname and not "ecg" in mapped:
chan.contains = "ecg"
elif "dz/dt" in cname or "derivative" in cname and \
not "dzdt" in mapped:
chan.contains = "dzdt"
elif "diastolic" in cname and not "diastolic" in mapped:
chan.contains = "diastolic"
elif "systolic" in cname and not "systolic" in mapped:
chan.contains = "systolic"
elif "blood pressure" in cname or "bp" in cname and \
not "bp" in mapped:
chan.contains = "bp"
elif "resp" in cname and not "respiration" in mapped:
chan.contains = "respiration"
elif "trigger" in cname and not "mri_trigger" in mapped:
chan.contains = "mri_trigger"
elif "stimulus" in cname and not "event" in mapped:
chan.contains = "event"
def subject_data(self):
return dict(subject_age = self.subject_age,
subject_gender = self.subject_gender,
subject_weight = self.subject_weight,
subject_height_ft = self.subject_height_ft,
subject_height_in = self.subject_height_in,
subject_electrode_distance_front = self.subject_electrode_distance_front,
subject_electrode_distance_back = self.subject_electrode_distance_back ,
subject_electrode_distance_left = self.subject_electrode_distance_left ,
subject_electrode_distance_right = self.subject_electrode_distance_right ,
subject_resp_max = self.subject_resp_max,
subject_resp_min = self.subject_resp_min,
subject_in_mri = self.subject_in_mri
)
def get_physiodata(self):
raise NotImplementedError("Must be overwritten by subclass")
class FMRITool(HasTraits):
physiodata = Instance(PhysioData)
processed_respiration_data = DelegatesTo("physiodata")
processed_respiration_time = DelegatesTo("physiodata")
slice_times_txt = Str
slice_times = Array
slice_times_matrix = Array
acquisition_type = Enum("Coronal", "Saggittal", "Axial")
dicom_acquisition_direction = Enum("LPS+", "RAS+")
unsure_about_direction = Bool(False)
correction_type = Enum(values="possible_corrections")
possible_corrections = List(["Slicewise Regression"])
respiration_expansion_order = Int(4)
drift_model_order = Int(6)
add_back_intensity = Bool(True)
cardiac_expansion_order = Int(3)
interaction_expansion_order = Int(1)
physio_design_file = File
# Local arrays that have been restricted to during-scanning times
r_times = Array # Beat times occurring during scanning
tr_onsets = Array # TR times
resp_times = Array
resp_signal = Array
# Nifti Stuff
fmri_file = File
fmri_mask = File
denoised_output = File
regression_output = File
nuisance_output_prefix = Str
b_calculate = Button(label="RUN")
write_4d_nuisance = Bool(False)
write_4d_nuisance_for_each_modality = Bool(False)
output_units = Enum("Percent Signal Change", "Raw BOLD")
fmri_tr = Float
interactive = Bool(False)
missing_triggers = Int(0)
missing_volumes = Int(0)
traits_view = MEAPView(VGroup(
VGroup(Item("fmri_file"),
Item("fmri_mask"),
Item("slice_times_txt"),
Item("acquisition_type"),
Item("dicom_acquisition_direction"),
Item("unsure_about_direction"),
Item("denoised_output"),
Item("regression_output"),
Item("nuisance_output_prefix"),
Item("write_4d_nuisance"),
Item("write_4d_nuisance_for_each_modality"),
show_border=True,
label="fMRI I/O"),
VGroup(Item("cardiac_expansion_order"),
Item("respiration_expansion_order"),
Item("interaction_expansion_order"),
Item("correction_type"),
Item("drift_model_order"),
Item("add_back_intensity"),
Item("output_units"),
Item("physio_design_file"),
show_border=True,
label="RETROICOR")),
Item("b_calculate", show_label=False),
win_title="RETROICOR")
def _load_slice_timings(self):
try:
_slices = np.loadtxt(self.slice_times_txt)
except Exception, e:
messagebox("Unable to load slice timings:\n%s" % e)
raise ValueError
# Check if it's in the mid-TR format
if np.any(_slices < 0):
logger.info("Using the mid-TR slice convention")
if self.fmri_tr <= 0:
raise ValueError("fMRI file has to be set before using mid-TR")
_slices = (_slices + 0.5) * self.fmri_tr
# Check if the times are in msec or
if np.any(_slices) > 10:
logger.info("Converting slice times from msec to sec")
_slices = _slices / 1000.
else:
logger.info("Assuming slice timings are in seconds")
# Slice times should be one row per TR, and one column
# per slice.
self.slice_times = _slices
logger.info("Using slice timings of %s", str(self.slice_times))
class TimeSeries(HasTraits):
# Holds data
name = Str
contains = Enum(SUPPORTED_SIGNALS)
plot = Instance(Plot, transient=True)
data = Array
time = Property(Array, depends_on=["start_time", "sampling_rate", "data"])
# Plotting options
visible = Bool(True)
ymax = Float()
ymin = Float()
line_type = marker_trait
line_color = ColorTrait("blue")
plot_type = Enum("line", "scatter")
censored_regions = List(Instance(CensorRegion))
b_add_censor = Button(label="Add CensorRegion", transient=True)
b_zoom_y = Button(label="Zoom y", transient=True)
b_info = Button(label="Info", transient=True)
b_clear_censoring = Button(label="Clear Censoring", transient=True)
renderer = Instance(LinePlot, transient=True)
# For the winsorizing steps
winsor_swap = Array
winsor_min = Float(0.005)
winsor_max = Float(0.005)
winsorize = Bool(False)
winsor_enable = Bool(True)
def __init__(self, **traits):
"""
Class to represent data collected over time
"""
super(TimeSeries, self).__init__(**traits)
if not self.contains in self.physiodata.contents:
raise ValueError("Signal not found in data")
self.name = self.contains
# First, check whether it's already winsorized
winsorize_trait = self.name + "_winsorize"
if getattr(self.physiodata, winsorize_trait):
self.winsor_enable = False
self.winsor_min = getattr(self.physiodata, self.name + "_winsor_min")
self.winsor_max = getattr(self.physiodata, self.name + "_winsor_max")
# Load the actual data
self.data = getattr(self.physiodata, self.contains + "_data")
self.winsor_swap = self.data.copy()
self.sampling_rate = getattr(self.physiodata,
self.contains + "_sampling_rate")
self.sampling_rate_unit = getattr(
self.physiodata, self.contains + "_sampling_rate_unit")
self.start_time = getattr(self.physiodata,
self.contains + "_start_time")
"""
The censored regions are loaded from physiodata INITIALLY.
from that point on the censored regions are accessed from
physiodata's
"""
self.line_color = colors[self.contains]
self.n_censor_intervals = 0
for (start, end), source in zip(self.physiodata.censored_intervals,
self.physiodata.censoring_sources):
if str(source) == self.contains:
self.censored_regions.append(
CensorRegion(start_time=start,
end_time=end,
metadata_name=self.__get_metadata_name()))
def __get_metadata_name(self):
name = self.contains + "%03d" % self.n_censor_intervals
self.n_censor_intervals += 1
return name
def _winsorize_changed(self):
if self.winsorize:
logger.info("Winsorizing %s with limits=(%.5f%.5f)", self.name,
self.winsor_min, self.winsor_max)
# Take the original data and replace it with the winsorized version
self.data = np.array(
winsorize(self.winsor_swap,
limits=(self.winsor_min, self.winsor_max)))
setattr(self.physiodata, self.name + "_winsor_min",
self.winsor_min)
setattr(self.physiodata, self.name + "_winsor_max",
self.winsor_max)
else:
logger.info("Restoring %s to its original data", self.name)
self.data = self.winsor_swap.copy()
setattr(self.physiodata, self.contains + "_data", self.data)
setattr(self.physiodata, self.name + "_winsorize", self.winsorize)
self.plot.range2d.y_range.low = self.data.min()
self.plot.range2d.y_range.high = self.data.max()
self.plot.request_redraw()
def __str__(self):
descr = "Timeseries: %s\n" % self.name
descr += "-" * len(descr) + "\n\t" + \
"\n\t".join([
"Sampling rate: %.4f%s" % (self.sampling_rate,self.sampling_rate_unit),
"N samples: %d" % self.data.shape[0],
"N censored intervals: %d" % len(self.censored_regions),
"Start time: %.3f" % self.start_time
])
return descr
def _plot_default(self):
# Create plotting components
plotdata = ArrayPlotData(time=self.time, data=self.data)
plot = Plot(plotdata)
self.renderer = plot.plot(("time", "data"), color=self.line_color)[0]
plot.title = self.name
plot.title_position = "right"
plot.title_angle = 270
plot.line_width = 1
plot.padding = 25
plot.width = 400
# Load the censor regions and add them to the plot
for censor_region in self.censored_regions:
# Make a censor region on the Timeseries object
censor_region.plot = self.renderer
censor_region.viz
censor_region.set_limits(censor_region.start_time,
censor_region.end_time)
return plot
def _get_time(self):
# Ensure the properties that depend on time are updated
return np.arange(len(self.data)) / self.sampling_rate + self.start_time
def _b_info_fired(self):
messagebox(str(self))
def _b_zoom_y_fired(self):
ui = self.edit_traits(view="zoom_view", kind="modal")
if ui.result:
self.plot.range2d.y_range.low = self.ymin
self.plot.range2d.y_range.high = self.ymax
def _b_clear_censoring_fired(self):
for reg in self.censored_regions:
self.renderer.overlays.remove(reg.viz)
self.censored_regions = []
self.plot.request_redraw()
self.n_censor_intervals = 0
def _b_add_censor_fired(self):
self.censored_regions.append(
CensorRegion(plot=self.renderer,
metadata_name=self.__get_metadata_name()))
self.censored_regions[-1].viz
buttons = VGroup(
Item("b_add_censor", show_label=False),
#Item("b_info"),
#Item("b_zoom_y"),
Item("winsorize", enabled_when="winsor_enable"),
Item("winsor_max",
enabled_when="winsor_enable",
format_str="%.4f",
width=25),
Item("winsor_min",
enabled_when="winsor_enable",
format_str="%.4f",
width=25),
Item("b_clear_censoring", show_label=False),
show_labels=True,
show_border=True)
widgets = HSplit(Item('plot', editor=ComponentEditor(), show_label=False),
buttons)
zoom_view = MEAPView(HGroup("ymin", "ymax"),
buttons=[OKButton, CancelButton])
traits_view = MEAPView(widgets, width=500, height=300, resizable=True)