.gitignore

@@ -0,0 +1,5 @@
+.coverage
+.cache
+__pycache__
+*.swp
+*.pyc

code/detect_events.py

@@ -1,229 +1,782 @@
 #!/usr/bin/python
 # -*- coding: iso-8859-15 -*-
 import numpy as np
+from statsmodels.robust.scale import mad
+from scipy import signal
 from scipy import ndimage
-import os
+from scipy.signal import savgol_filter # Savitzky–Golay filter, for smoothing data
-from os.path import join as opj
+from scipy.ndimage import median_filter
 import sys
 import gzip
-from os.path import basename
+from math import (
-from os.path import exists
+    degrees,
-from glob import glob
+    atan2,
+)
 
-#infile = sys.argv[1]
+import logging
-#outfile = sys.argv[2]
+lgr = logging.getLogger('studyforrest.detect_eyegaze_events')
 
-def get_signal_props(data, px2deg):
+
+def deg_per_pixel(screen_size, viewing_distance, screen_resolution):
+    """Determine `px2deg` factor for EyegazeClassifier
+
+    Parameters
+    ----------
+    screen_size : float
+      Either vertical or horizontal dimension of the screen in any unit.
+    viewing_distance : float
+      Viewing distance from the screen in the same unit as `screen_size`.
+    screen_resolution : int
+      Number of pixels along the dimensions reported for `screen_size`.
+    """
+    return degrees(atan2(.5 * screen_size, viewing_distance)) / \
+        (.5 * screen_resolution)
+
+
+def find_peaks(vels, threshold):
+    """Find above-threshold time periods
+
+    Parameters
+    ----------
+    vels : array
+      Velocities.
+    threshold : float
+      Velocity threshold.
+
+    Returns
+    -------
+    list
+      Each item is a tuple with start and end index of the window where
+      velocities exceed the threshold.
+    """
+    def _get_vels(start, end):
+        v = vels[start:end]
+        v = v[~np.isnan(v)]
+        return v
+
+    sacs = []
+    sac_on = None
+    for i, v in enumerate(vels):
+        if sac_on is None and v > threshold:
+            # start of a saccade
+            sac_on = i
+        elif sac_on is not None and v < threshold:
+            sacs.append([
+                sac_on,
+                i,
+                _get_vels(
+                    sac_on,
+                    min(len(vels), i + 1))
+            ])
+            sac_on = None
+    if sac_on:
+        # end of data, but velocities still high
+        sacs.append([
+            sac_on,
+            len(vels) - 1,
+            _get_vels(sac_on, len(vels))])
+    return sacs
+
+
+def find_saccade_onsetidx(vels, start_idx, sac_onset_velthresh):
+    idx = start_idx
+    while idx > 0 \
+            and (vels[idx] > sac_onset_velthresh or
+                 vels[idx] <= vels[idx - 1]):
+        # find first local minimum after vel drops below onset threshold
+        # going backwards in time
+
+        # we used to do this, but it could mean detecting very long
+        # saccades that consist of (mostly) missing data
+        #         or np.isnan(vels[sacc_start])):
+        idx -= 1
+    return idx
+
+
+def find_movement_offsetidx(vels, start_idx, off_velthresh):
+    idx = start_idx
+    # shift saccade end index to the first element that is below the
+    # velocity threshold
+    while idx < len(vels) - 1 \
+            and (vels[idx] > off_velthresh or
+                 (vels[idx] > vels[idx + 1])):
+            # we used to do this, but it could mean detecting very long
+            # saccades that consist of (mostly) missing data
+            #    or np.isnan(vels[idx])):
+        idx += 1
+    return idx
+
+
+def find_psoend(velocities, sac_velthresh, sac_peak_velthresh):
+        pso_peaks = find_peaks(velocities, sac_peak_velthresh)
+        if pso_peaks:
+            pso_label = 'HPSO'
+        else:
+            pso_peaks = find_peaks(velocities, sac_velthresh)
+            if pso_peaks:
+                pso_label = 'LPSO'
+        if not pso_peaks:
+            # no PSO
+            return
+
+        # find minimum after the offset of the last reported peak
+        pso_end = find_movement_offsetidx(
+            velocities, pso_peaks[-1][1], sac_velthresh)
+
+        if pso_end > len(velocities):
+            # velocities did not go down within the given window
+            return
+
+        return pso_label, pso_end
+
+
+def filter_spikes(data):
+    """In-place high-frequency spike filter
+
+    Inspired by:
+
+      Stampe, D. M. (1993). Heuristic filtering and reliable calibration
+      methods for video-based pupil-tracking systems. Behavior Research
+      Methods, Instruments, & Computers, 25(2), 137–142.
+      doi:10.3758/bf03204486
+    """
+    def _filter(arr):
+        # over all triples of neighboring samples
+        for i in range(1, len(arr) - 1):
+            if (arr[i - 1] < arr[i] and arr[i] > arr[i + 1]) \
+                    or (arr[i - 1] > arr[i] and arr[i] < arr[i + 1]):
+                # immediate sign-reversal of the difference from
+                # x-1 -> x -> x+1
+                prev_dist = abs(arr[i - 1] - arr[i])
+                next_dist = abs(arr[i + 1] - arr[i])
+                # replace x by the neighboring value that is closest
+                # in value
+                arr[i] = arr[i - 1] \
+                    if prev_dist < next_dist else arr[i + 1]
+        return arr
+
+    data['x'] = _filter(data['x'])
+    data['y'] = _filter(data['y'])
+    return data
+
+
+def get_dilated_nan_mask(arr, iterations, max_ignore_size=None):
+    clusters, nclusters = ndimage.label(np.isnan(arr))
+    # go through all clusters and remove any cluster that is less
+    # the max_ignore_size
+    for i in range(nclusters):
+        # cluster index is base1
+        i = i + 1
+        if (clusters == i).sum() <= max_ignore_size:
+            clusters[clusters == i] = 0
+    # mask to cover all samples with dataloss > `max_ignore_size`
+    mask = ndimage.binary_dilation(clusters > 0, iterations=iterations)
+    return mask
+
+
+
+class EyegazeClassifier(object):
+
+    record_field_names = [
+        'id', 'label',
+        'start_time', 'end_time',
+        'start_x', 'start_y',
+        'end_x', 'end_y',
+        'amp', 'peak_vel', 'avg_vel',
+    ]
+
+    def __init__(self,
+                 px2deg,
+                 sampling_rate,
+                 velthresh_startvelocity=300.0,
+                 min_intersaccade_duration=0.04,
+                 min_saccade_duration=0.01,
+                 max_initial_saccade_freq=2.0,
+                 saccade_context_window_length=1.0,
+                 max_pso_duration=0.04,
+                 min_fixation_duration=0.04,
+                 max_fixation_amp=0.7):
+            self.px2deg = px2deg
+            self.sr = sr = sampling_rate
+            self.velthresh_startvel = velthresh_startvelocity
+            self.max_fix_amp = max_fixation_amp
+
+            # convert to #samples
+            self.min_intersac_dur = int(
+                min_intersaccade_duration * sr)
+            self.min_sac_dur = int(
+                min_saccade_duration * sr)
+            self.sac_context_winlen = int(
+                saccade_context_window_length * sr)
+            self.max_pso_dur = int(
+                max_pso_duration * sr)
+            self.min_fix_dur = int(
+                min_fixation_duration * sr)
+
+            self.max_sac_freq = max_initial_saccade_freq / sr
+
+    # TODO dissolve
+    def _get_signal_props(self, data):
         data = data[~np.isnan(data['vel'])]
         pv = data['vel'].max()
         amp = (((data[0]['x'] - data[-1]['x']) ** 2 + \
-            (data[0]['y'] - data[-1]['y']) ** 2) ** 0.5) * px2deg
+                (data[0]['y'] - data[-1]['y']) ** 2) ** 0.5) * self.px2deg
-    avVel = data['vel'].mean()
+        medvel = np.median(data['vel'])
-    return pv, amp, avVel
+        return amp, pv, medvel
 
+    def get_adaptive_saccade_velocity_velthresh(self, vels):
+        """Determine saccade peak velocity threshold.
 
-def detect(infile, outfile, fixation_threshold, px2deg):
+        Takes global noise-level of data into account. Implementation
-    data = np.recfromcsv(
+        based on algorithm proposed by NYSTROM and HOLMQVIST (2010).
-        infile,
-        delimiter='\t',
-        names=['vel', 'accel', 'x', 'y'])
-    print ("Data length", len(data))
 
-    out=gzip.open(outfile,"wb")
+        Parameters
+        ----------
+        start : float
+          Start velocity for adaptation algorithm. Should be larger than
+          any conceivable minimal saccade velocity (in deg/s).
+        TODO std unit multipliers
 
-#####get threshold function #######
+        Returns
-    newThr=200                              # What is this "threshold"?
+        -------
-    def getThresh(cut):                     # def refers to defining your own function; cut is input arg
+        tuple
-        vel_uthr = data['vel'][data['vel'] < cut]
+          (peak saccade velocity threshold, saccade onset velocity threshold).
-        avg = vel_uthr.mean()
+          The latter (and lower) value can be used to determine a more precise
-        sd = vel_uthr.std()
+          saccade onset.
-        return avg+6*sd, avg, sd            # outputs of function; average+6*sd denotes a RANGE in any normal distribution
+        """
+        cur_thresh = self.velthresh_startvel
 
-###### threshold function #########      NYSTROM and HOLMQVIST (2010) ALGORITHM IS USED to find a suitable threshold  
+        def _get_thresh(cut):
+            # helper function
+            vel_uthr = vels[vels < cut]
+            med = np.median(vel_uthr)
+            scale = mad(vel_uthr)
+            return med + 10 * scale, med, scale
 
-    dif=2
+        # re-compute threshold until value converges
-    while dif > 1:
+        count = 0
-        oldThr = newThr                      #Threshold in 100-300 degree/sec. 200 here.
+        dif = 2
-        newThr, avg, sd = getThresh(oldThr)  #Average and std is calculated and Thr is renewed
+        while dif > 1 and count < 30:  # less than 1deg/s difference
-        dif= abs(oldThr - newThr)           #return absolute value, keep doing the loop until PTn-PTn-1 is smaller than 1 degree
+            old_thresh = cur_thresh
+            cur_thresh, med, scale = _get_thresh(old_thresh)
+            if not cur_thresh:
+                # safe-guard in case threshold runs to zero in
+                # case of really clean and sparse data
+                cur_thresh = old_thresh
+                break
+            lgr.debug(
+                'Saccade threshold velocity: %.1f '
+                '(non-saccade mvel: %.1f, stdvel: %.1f)',
+                cur_thresh, med, scale)
+            dif = abs(old_thresh - cur_thresh)
+            count += 1
 
-    threshold=newThr
+        return cur_thresh, (med + 5 * scale)
-    soft_threshold = avg + 3 * sd
-    print("after thr selection", threshold)
 
+    def _mk_event_record(self, data, idx, label, start, end):
+        return dict(zip(self.record_field_names, (
+            idx,
+            label,
+            start,
+            end,
+            data[start]['x'],
+            data[start]['y'],
+            data[end - 1]['x'],
+            data[end - 1]['y']) +
+            self._get_signal_props(data[start:end])))
 
-####get peaks#### Saccade by definition, is the first velocity that goes above the saccade threshold (NOT VELOCITY threshold)
+    def __call__(self, data, classify_isp=True, sort_events=True):
-    peaks=[]
+        # find threshold velocities
+        sac_peak_med_velthresh, sac_onset_med_velthresh = \
+            self.get_adaptive_saccade_velocity_velthresh(data['med_vel'])
+        lgr.info(
+            'Global saccade MEDIAN velocity thresholds: '
+            '%.1f, %.1f (onset, peak)',
+            sac_onset_med_velthresh, sac_peak_med_velthresh)
 
-    peaks = np.where(
+        saccade_locs = find_peaks(
-        np.logical_and(
+            data['med_vel'],
-            data['vel'][:-1] < threshold,
+            sac_peak_med_velthresh)
-            data['vel'][1:] > threshold))[0]
-    # XXX original code had [0] at index 1
-    # XXX really?! why 1
-    peaks += 1
 
-    above_thr_clusters, nclusters = ndimage.label(data['vel'] > soft_threshold)
-    if not nclusters:
-        print('Got no above threshold values, baby. Going home...')
-        return
-    # reinclude any timepoint that has missing data, and treat it as above threshold
-    # XXX could this possibly introduce fake saccades? MIH think not, but isnt sure
-    above_thr_clusters[np.isnan(data['vel'])] = 1
-
-    fix=[]
         events = []
+        saccade_events = []
+        for e in self._detect_saccades(
+                saccade_locs,
+                data,
+                0,
+                len(data),
+                context=self.sac_context_winlen):
+            saccade_events.append(e.copy())
+            events.append(e)
 
-    print (peaks)
+        lgr.info('Start ISP classification')
 
-    for i, pos in enumerate(peaks):
+        if classify_isp:
-        sacc_start = pos
+            events.extend(self._classify_intersaccade_periods(
-        while sacc_start > 0 and above_thr_clusters[sacc_start] > 0:
+                data,
-            sacc_start -= 1
+                0,
+                len(data),
+                # needs to be in order of appearance
+                sorted(saccade_events, key=lambda x: x['start_time']),
+                saccade_detection=True))
 
-        # TODO: make sane
+        # make timing info absolute times, not samples
-        fix.append(-(sacc_start - 1))  # this is chinese for saying "I am not a fixation anymore"
-
-        off_period_vel = data['vel'][sacc_start - 41:sacc_start]
-        # exclude NaN
-        off_period_vel = off_period_vel[~np.isnan(off_period_vel)]
-        # go with adaptive threshold, but only if the 40ms prior to the saccade have some
-        # data to compute a velocity stdev from
-        off_threshold = (0.7 * soft_threshold) + \
-                        (0.3 * (np.mean(off_period_vel) + 3 * np.std(off_period_vel))) \
-                        if len(off_period_vel) > 40 else soft_threshold
-
-        sacc_end = pos
-        while sacc_end < len(data) - 1 > 0 and \
-                (data['vel'][sacc_end] > off_threshold or \
-                 np.isnan(data['vel'][sacc_end])):
-            sacc_end += 1
-        # mark start of a fixation
-        fix.append(sacc_end)
-
-        # minimum duration 9 ms and no blinks allowed (!) If we increase this then saccades higher than 9ms will be considered as fixations too --- we can now get the "short" saccades
-        
-        if sacc_end - sacc_start >= 21 and\
-                not np.sum(np.isnan(data['x'][sacc_start:sacc_end])):
-            sacc_data = data[sacc_start:sacc_end]
-            pv, amp, avVel = get_signal_props(sacc_data, px2deg)
-            sacc_duration = sacc_end - sacc_start
-            events.append((
-                "SACCADE",
-                sacc_start,
-                sacc_end,
-                sacc_data[0]['x'],
-                sacc_data[0]['y'],
-                sacc_data[-1]['x'],
-                sacc_data[-1]['y'],
-                amp,
-                pv,
-                avVel,
-                sacc_duration))
-        # The rest of the shorter saccades will be assigned as "FIX"'s as well. 
-        # Note: they may become indistinguisble from our events that meet the formal fixation criterion.
-        # Could call them something else "PURSUIT" ?
-        
-        elif sacc_end - sacc_start < 21 and sacc_end - sacc_start > 9 and\
-                not np.sum(np.isnan(data['x'][sacc_start:sacc_end])):
-            sacc_data = data[sacc_start:sacc_end]
-            pv, amp, avVel = get_signal_props(sacc_data, px2deg)
-            sacc_duration = sacc_end - sacc_start
-            events.append((
-                "FIX",
-                sacc_start,
-                sacc_end,
-                sacc_data[0]['x'],
-                sacc_data[0]['y'],
-                sacc_data[-1]['x'],
-                sacc_data[-1]['y'],
-                amp,
-                pv,
-                avVel,
-                sacc_duration))
-                
-######## end of saccade detection = begin of glissade detection ########
-
-        idx = sacc_end + 1
-#        below=False
-#        offset=False
-        # pval=[]
-        #sacc_data
-
-        gldata = data[sacc_end:sacc_end + 40]
-        # going from the end of the window to find the last match
-        for i in range(0, len(gldata) - 2):
-            # velocity after saccade end goes below the soft threshold
-            # and immediately afterwards stay or increases the velocity again
-            if gldata[(-1 * i) - 2]['vel'] < soft_threshold and \
-                    gldata[(-1 * i) - 1]['vel'] > soft_threshold and \
-                    gldata[(-1 * i) -3]['vel'] >= gldata[(-1 * i) -2]['vel']:
-                gliss_data = gldata[:-i]
-                gliss_end = sacc_end + len(gldata) - i
-
-                if not len(gliss_data) or np.sum(np.isnan(gliss_data['vel'])) > 10:
-                    # not more than 10 ms of signal loss in glissades
-                    break
-                pv, amp, avVel = get_signal_props(gliss_data, px2deg)
-                gl_duration = gliss_end - (sacc_end + 1)
-                events.append((
-                    "GLISSADE",
-                    sacc_end + 1,
-                    gliss_end,
-                    gldata[0]['x'],
-                    gldata[0]['y'],
-                    gldata[-i]['x'],
-                    gldata[-1]['y'],
-                    amp,
-                    pv,
-                    avVel,
-                    gl_duration))
-                fix.pop()
-                fix.append(gliss_end)
-                break
-
-######### fixation detection after everything else is identified ########
-
-    for j, f in enumerate(fix[:-1]):
-        fix_start = f
-        # end times are coded negative
-        fix_end = abs(fix[j + 1])
-        if f > 0 and fix_end - f > 40:          #onset of fixation
-            fixdata = data[f:fix_end]
-            if not len(fixdata) or np.isnan(fixdata[0][0]):
-                print("Erroneous fixation interval")
-                continue
-            pv, amp, avVel = get_signal_props(fixdata, px2deg)
-            fix_duration = fix_end - f
-
-            if avVel < fixation_threshold and amp < 2 and np.sum(np.isnan(fixdata['vel'])) <= 10:
-                events.append((
-                    "FIX",
-                    f,
-                    fix[j + 1],
-                    data[f]['x'],
-                    data[f]['y'],
-                    data[fix_end]['x'],
-                    data[fix_end]['y'],
-                    amp,
-                    pv,
-                    avVel,
-                    fix_duration))
-
-
-    # TODO think about just saving it in binary form
-    f = gzip.open (outfile, "w")
         for e in events:
-        f.write('%s\t%i\t%i\t%f\t%f\t%f\t%f\t%f\t%f\t%f\t%f\n' % e)
+            for i in ('start_time', 'end_time'):
-    print ("done")
+                e[i] = e[i] / self.sr
+
+        return sorted(events, key=lambda x: x['start_time']) \
+            if sort_events else events
+
+    def _detect_saccades(
+            self,
+            candidate_locs,
+            data,
+            start,
+            end,
+            context):
+
+        saccade_events = []
+
+        if context is None:
+            # no context size was given, use all data
+            # to determine velocity thresholds
+            lgr.debug(
+                'Determine velocity thresholds on full segment '
+                '[%i, %i]', start, end)
+            sac_peak_velthresh, sac_onset_velthresh = \
+                self.get_adaptive_saccade_velocity_velthresh(
+                    data['vel'][start:end])
+            if candidate_locs is None:
+                lgr.debug(
+                    'Find velocity peaks on full segment '
+                    '[%i, %i]', start, end)
+                candidate_locs = [
+                    (e[0] + start, e[1] + start, e[2]) for e in find_peaks(
+                        data['vel'][start:end],
+                        sac_peak_velthresh)]
+
+        # status map indicating which event class any timepoint has been
+        # assigned to so far
+        status = np.zeros((len(data),), dtype=int)
+
+        # loop over all peaks sorted by the sum of their velocities
+        # i.e. longer and faster goes first
+        for i, props in enumerate(sorted(
+                candidate_locs, key=lambda x: x[2].sum(), reverse=True)):
+            sacc_start, sacc_end, peakvels = props
+            lgr.info(
+                'Process peak velocity window [%i, %i] at ~%.1f deg/s',
+                sacc_start, sacc_end, peakvels.mean())
+
+            if context:
+                # extract velocity data in the vicinity of the peak to
+                # calibrate threshold
+                win_start = max(
+                    start,
+                    sacc_start - int(context / 2))
+                win_end = min(
+                    end,
+                    sacc_end + context - (sacc_start - win_start))
+                lgr.debug(
+                    'Determine velocity thresholds in context window '
+                    '[%i, %i]', win_start, win_end)
+                lgr.debug('Actual context window: [%i, %i] -> %i',
+                          win_start, win_end, win_end - win_start)
+
+                sac_peak_velthresh, sac_onset_velthresh = \
+                    self.get_adaptive_saccade_velocity_velthresh(
+                        data['vel'][win_start:win_end])
+
+            lgr.info('Active saccade velocity thresholds: '
+                     '%.1f, %.1f (onset, peak)',
+                     sac_onset_velthresh, sac_peak_velthresh)
+
+            # move backwards in time to find the saccade onset
+            sacc_start = find_saccade_onsetidx(
+                data['vel'], sacc_start, sac_onset_velthresh)
+
+            # move forward in time to find the saccade offset
+            sacc_end = find_movement_offsetidx(
+                data['vel'], sacc_end, sac_onset_velthresh)
+
+            sacc_data = data[sacc_start:sacc_end]
+            if sacc_end - sacc_start < self.min_sac_dur:
+                lgr.debug('Skip saccade candidate, too short')
+                continue
+            elif np.sum(np.isnan(sacc_data['x'])):  # pragma: no cover
+                # should not happen
+                lgr.debug('Skip saccade candidate, missing data')
+                continue
+            elif status[
+                    max(0,
+                        sacc_start - self.min_intersac_dur):min(
+                    len(data), sacc_end + self.min_intersac_dur)].sum():
+                lgr.debug('Skip saccade candidate, too close to another event')
+                continue
+
+            lgr.debug('Found SACCADE [%i, %i]',
+                      sacc_start, sacc_end)
+            event = self._mk_event_record(data, i, "SACC", sacc_start, sacc_end)
+
+            yield event.copy()
+            saccade_events.append(event)
+
+            # mark as a saccade
+            status[sacc_start:sacc_end] = 1
+
+            pso = find_psoend(
+                data['vel'][sacc_end:sacc_end + self.max_pso_dur],
+                sac_onset_velthresh,
+                sac_peak_velthresh)
+            if pso:
+                pso_label, pso_end = pso
+                lgr.debug('Found %s [%i, %i]',
+                          pso_label, sacc_end, pso_end)
+                psoevent = self._mk_event_record(
+                    data, i, pso_label, sacc_end, sacc_end + pso_end)
+                if psoevent['amp'] < saccade_events[-1]['amp']:
+                    # discard PSO with amplitudes larger than their
+                    # anchor saccades
+                    yield psoevent.copy()
+                    # mark as a saccade part
+                    status[sacc_end:sacc_end + pso_end] = 1
+                else:
+                    lgr.debug(
+                        'Ignore PSO, amplitude large than that of '
+                        'the previous saccade: %.1f >= %.1f',
+                        psoevent['amp'], saccade_events[-1]['amp'])
+
+            if self.max_sac_freq and \
+                    float(len(saccade_events)) / len(data) > self.max_sac_freq:
+                lgr.info('Stop initial saccade detection, max frequency '
+                         'reached')
+                break
+
+    def _classify_intersaccade_periods(
+            self,
+            data,
+            start,
+            end,
+            saccade_events,
+            saccade_detection):
+
+        lgr.warn(
+            'Determine ISPs %i, %i (%i saccade-related events)',
+            start, end, len(saccade_events))
+
+        prev_sacc = None
+        prev_pso = None
+        for ev in saccade_events:
+            if prev_sacc is None:
+                if 'SAC' not in ev['label']:
+                    continue
+            elif prev_pso is None and 'PS' in ev['label']:
+                prev_pso = ev
+                continue
+            elif 'SAC' not in ev['label']:
+                continue
+
+            # at this point we have a previous saccade (and possibly its PSO)
+            # on record, and we have just found the next saccade
+            # -> inter-saccade window is determined
+            if prev_sacc is None:
+                win_start = start
+            else:
+                if prev_pso is not None:
+                    win_start = prev_pso['end_time']
+                else:
+                    win_start = prev_sacc['end_time']
+            # enforce dtype for indexing
+            win_end = ev['start_time']
+            if win_start == win_end:
+                prev_sacc = ev
+                prev_pso = None
+                continue
+
+            lgr.warn('Found ISP [%i:%i]', win_start, win_end)
+            for e in self._classify_intersaccade_period(
+                    data,
+                    win_start,
+                    win_end,
+                    saccade_detection=saccade_detection):
+                yield e
+
+            # lastly, the current saccade becomes the previous one
+            prev_sacc = ev
+            prev_pso = None
+
+        if prev_sacc is not None and prev_sacc['end_time'] == end:
+            return
+
+        lgr.debug("LAST_SEGMENT_ISP: %s -> %s", prev_sacc, prev_pso)
+        # and for everything beyond the last saccade (if there was any)
+        for e in self._classify_intersaccade_period(
+                data,
+                start if prev_sacc is None
+                else prev_sacc['end_time'] if prev_pso is None
+                else prev_pso['end_time'],
+                end,
+                saccade_detection=saccade_detection):
+            yield e
+
+    def _classify_intersaccade_period(
+            self,
+            data,
+            start,
+            end,
+            saccade_detection):
+        lgr.warn('Determine NaN-free intervals in [%i:%i] (%i)',
+                 start, end, end - start)
+
+        # split the ISP up into its non-NaN pieces:
+        win_start = None
+        for idx in range(start, end + 1):
+            if win_start is None and not np.isnan(data['x'][idx]):
+                win_start = idx
+            elif win_start is not None and \
+                    ((idx == end) or np.isnan(data['x'][idx])):
+                for e in self._classify_intersaccade_period_helper(
+                        data,
+                        win_start,
+                        idx,
+                        saccade_detection):
+                    yield e
+                # reset non-NaN window start
+                win_start = None
+
+    def _classify_intersaccade_period_helper(
+            self,
+            data,
+            start,
+            end,
+            saccade_detection):
+        # no NaN values in data at this point!
+        lgr.warn(
+            'Process non-NaN segment [%i, %i] -> %i',
+            start, end, end - start)
+
+        label_remap = {
+            'SACC': 'ISAC',
+            'HPSO': 'IHPS',
+            'LPSO': 'ILPS',
+        }
+
+        length = end - start
+        # detect saccades, if the there is enough space to maintain minimal
+        # distance to other saccades
+        if length > (
+                2 * self.min_intersac_dur) \
+                + self.min_sac_dur + self.max_pso_dur:
+            lgr.warn('Perform saccade detection in [%i:%i]', start, end)
+            saccades = self._detect_saccades(
+                None,
+                data,
+                start,
+                end,
+                context=None)
+            saccade_events = []
+            if saccades is not None:
+                kill_pso = False
+                for s in saccades:
+                    if kill_pso:
+                        kill_pso = False
+                        if s['label'].endswith('PSO'):
+                            continue
+                    if s['start_time'] - start < self.min_intersac_dur or \
+                            end - s['end_time'] < self.min_intersac_dur:
+                        # to close to another saccade
+                        kill_pso = True
+                        continue
+                    s['label'] = label_remap.get(s['label'], s['label'])
+                    # need to make a copy of the dict to not have outside
+                    # modification interfere with further inside processing
+                    yield s.copy()
+                    saccade_events.append(s)
+            if saccade_events:
+                lgr.warn('Found additional saccades in ISP')
+                # and now process the intervals between the saccades
+                for e in self._classify_intersaccade_periods(
+                        data,
+                        start,
+                        end,
+                        sorted(saccade_events,
+                               key=lambda x: x['start_time']),
+                        saccade_detection=False):
+                    yield e
+                return
+
+        max_amp, label = self._fix_or_pursuit(data, start, end)
+        if label is not None:
+            yield self._mk_event_record(
+                data,
+                max_amp,
+                label,
+                start,
+                end)
+
+    def _fix_or_pursuit(self, data, start, end):
+        win_data = data[start:end].copy()
+
+        if len(win_data) < self.min_fix_dur:
+            return None, None
+
+        def _butter_lowpass(cutoff, fs, order=5):
+            nyq = 0.5 * fs
+            normal_cutoff = cutoff / nyq
+            b, a = signal.butter(
+                order,
+                normal_cutoff,
+                btype='low',
+                analog=False)
+            return b, a
+
+        b, a = _butter_lowpass(10.0, 1000.0)
+        win_data['x'] = signal.filtfilt(b, a, win_data['x'], method='gust')
+        win_data['y'] = signal.filtfilt(b, a, win_data['y'], method='gust')
+
+        win_data = win_data[10:-10]
+        start_x = win_data[0]['x']
+        start_y = win_data[0]['y']
+
+        # determine max location deviation from start coordinate
+        amp = (((start_x - win_data['x']) ** 2 +
+                (start_y - win_data['y']) ** 2) ** 0.5)
+        amp_argmax = amp.argmax()
+        max_amp = amp[amp_argmax] * self.px2deg
+        #print('MAX IN WIN [{}:{}]@{:.1f})'.format(start, end, max_amp))
+
+        if max_amp > self.max_fix_amp:
+            return max_amp, 'PURS'
+        return max_amp, 'FIXA'
+
+    def preproc(
+            self,
+            data,
+            min_blink_duration=0.02,
+            dilate_nan=0.01,
+            median_filter_length=0.05,
+            savgol_length=0.019,
+            savgol_polyord=2,
+            max_vel=1000.0):
+        """
+        Parameters
+        ----------
+        data : array
+          Record array with fields ('x', 'y', 'pupil')
+        px2deg : float
+          Size of a pixel in visual angles.
+        min_blink_duration : float
+          In seconds. Any signal loss shorter than this duration with not be
+          considered for `dilate_blink`.
+        dilate_blink : float
+          Duration by which to dilate a blink window (missing data segment) on
+          either side (in seconds).
+        median_filter_width : float
+          Filter window length in seconds.
+        savgol_length : float
+          Filter window length in seconds.
+        savgol_polyord : int
+          Filter polynomial order used to fit the samples.
+        sampling_rate : float
+          In Hertz
+        max_vel : float
+          Maximum velocity in deg/s. Any velocity value larger than this threshold
+          will be replaced by the previous velocity value. Additionally a warning
+          will be issued to indicate a potentially inappropriate filter setup.
+        """
+        # convert params in seconds to #samples
+        dilate_nan = int(dilate_nan * self.sr)
+        min_blink_duration = int(min_blink_duration * self.sr)
+        savgol_length = int(savgol_length * self.sr)
+        median_filter_length = int(median_filter_length * self.sr)
+
+        # in-place spike filter
+        data = filter_spikes(data)
+
+        # for signal loss exceeding the minimum blink duration, add additional
+        # dilate_nan at either end
+        # find clusters of "no data"
+        if dilate_nan:
+            mask = get_dilated_nan_mask(
+                data['x'],
+                dilate_nan,
+                min_blink_duration)
+            data['x'][mask] = np.nan
+            data['y'][mask] = np.nan
+
+        if savgol_length:
+            for i in ('x', 'y'):
+                data[i] = savgol_filter(data[i], savgol_length, savgol_polyord)
+
+        # velocity calculation, exclude velocities over `max_vel`
+        # euclidean distance between successive coordinate samples
+        # no entry for first datapoint!
+        velocities = (np.diff(data['x']) ** 2 + np.diff(data['y']) ** 2) ** 0.5
+        # convert from px/sample to deg/s
+        velocities *= self.px2deg * self.sr
+
+        if median_filter_length:
+            med_velocities = np.zeros((len(data),), velocities.dtype)
+            med_velocities[1:] = (
+                np.diff(median_filter(data['x'],
+                                      size=median_filter_length)) ** 2 +
+                np.diff(median_filter(data['y'],
+                                      size=median_filter_length)) ** 2) ** 0.5
+            # convert from px/sample to deg/s
+            med_velocities *= self.px2deg * self.sr
+            # remove any velocity bordering NaN
+            med_velocities[get_dilated_nan_mask(
+                med_velocities, dilate_nan, 0)] = np.nan
+
+        # replace "too fast" velocities with previous velocity
+        # add missing first datapoint
+        filtered_velocities = [float(0)]
+        for vel in velocities:
+            if vel > max_vel:  # deg/s
+                # ignore very fast velocities
+                lgr.warning(
+                    'Computed velocity exceeds threshold. '
+                    'Inappropriate filter setup? [%.1f > %.1f deg/s]',
+                    vel,
+                    max_vel)
+                vel = filtered_velocities[-1]
+            filtered_velocities.append(vel)
+        velocities = np.array(filtered_velocities)
+
+        # acceleration is change of velocities over the last time unit
+        acceleration = np.zeros(velocities.shape, velocities.dtype)
+        acceleration[1:] = (velocities[1:] - velocities[:-1]) * self.sr
+
+        arrs = [med_velocities] if median_filter_length else []
+        names = ['med_vel'] if median_filter_length else []
+        arrs.extend([
+            velocities,
+            acceleration,
+            data['x'],
+            data['y']])
+        names.extend(['vel', 'accel', 'x', 'y'])
+        return np.core.records.fromarrays(arrs, names=names)
 
 
 if __name__ == '__main__':
-    fixation_threshold = float(sys.argv[1])
+    fixation_velthresh = float(sys.argv[1])
     px2deg = float(sys.argv[2])
     infpath = sys.argv[3]
     outfpath = sys.argv[4]
-    detect(infpath, outfpath, fixation_threshold, px2deg)
+    data = np.recfromcsv(
+        infpath,
+        delimiter='\t',
+        names=['vel', 'accel', 'x', 'y'])
+
+    events = detect(data, outfpath, fixation_velthresh, px2deg)
+
+    # TODO think about just saving it in binary form
+    f = gzip.open(outfpath, "w")
+    for e in events:
+        f.write('%s\t%i\t%i\t%f\t%f\t%f\t%f\t%f\t%f\t%f\t%f\n' % e)
+
+
 
 
 

code/pixel_to_angle.py

@@ -1,37 +0,0 @@
-# Sebastiaan Mathot (modified)
-# -*- coding: iso-8859-15 -*-
-
-
-from math import atan2, degrees
-h = 52.2 # Monitor width in cm, this is the BEH screen
-d = 85 # Distance between monitor and participant in cm
-r = 1280 # Horizontal resolution of the monitor
-size_in_px = 1 # The stimulus size in pixels
-# Calculate the number of degrees that correspond to a single pixel. This will
-# generally be a very small value, something like 0.03.
-deg_per_px = degrees(atan2(.5*h, d)) / (.5*r)
-print '%s degrees correspond to a single pixel' % deg_per_px
-# Calculate the size of the stimulus in degrees
-size_in_deg = size_in_px * deg_per_px
-print 'The size of the stimulus is %s pixels and %s visual degrees' \
-    % (size_in_px, size_in_deg)
-
-
-#h = 26.5 # Monitor width in cm 
-#d = 63 # Distance between monitor and participant in cm
-#This is for the MRI screen
-
-#Checking from paper
-#MRI
-#In [1]: 0.0185581232561*1280
-#Out[1]: 23.754397767808
-#BEH
-#In [2]: 0.0266711972026*1280
-#Out[2]: 34.139132419328
-
-#Calculating the ratio
-#In [7]: 0.0185581232561*0.01
-#Out[7]: 0.000185581232561
-
-#In [8]: 0.000185581232561/0.0266711972026
-#Out[8]: 0.006958114071568895

code/preprocess_eyegaze_recordings.py

@@ -1,98 +0,0 @@
-#!/usr/bin/python
-# -*- coding: iso-8859-15 -*-
-
-import sys
-import numpy as np
-from scipy.signal import savgol_filter # Savitzky–Golay filter, for smoothing data
-from scipy import ndimage as ndimage
-from glob import glob                  # The glob.glob returns the list of files with their full path
-import gzip
-import os
-from os.path import basename           # returns the tail of the path
-from os.path import dirname
-from os.path import curdir
-from os.path import exists             # logical for if a certain file exists
-from os.path import join as opj
-
-sampling_rate = 1000.0  # in Hertz
-
-
-def preproc(infile, outfile, px2deg):
-    # TODO parameter
-    # max_signal_loss_without_something
-    # blank_duration
-    # savgol_window_length
-    # savgol_polyord
-    # savgol_iterations
-
-    outdir = dirname(outfile)
-    outdir = curdir if not outdir else outdir
-    if not exists(outdir):
-        os.makedirs(outdir)
-
-    data = np.recfromcsv(
-        infile,
-        delimiter='\t',
-        names=['x', 'y', 'pupil', 'frame'])
-
-    # for signal loss exceeding 20 ms, additional 10 ms at beginning
-    # find clusters of "no data"
-    clusters, nclusters = ndimage.label(np.isnan(data['x']))
-    # go through all clusters and remove any cluster that is less than 20 samples
-    for i in range(1, nclusters):
-        if (clusters == i).sum() <= 20:
-            clusters[clusters == i] = 0
-    # mask to cover all samples with dataloss > 20ms, plus 10 samples on either
-    # side of the lost segment
-    mask = ndimage.binary_dilation(clusters > 0, iterations=10)
-    data['x'][mask] = np.nan
-    data['y'][mask] = np.nan
-    data['pupil'][mask] = np.nan
-
-    # TODO filtering with NaNs in place kicks out additional datapoints, maybe
-    # do no or less dilation of the mask above
-    data['x'] = savgol_filter(data['x'], 19, 1)
-    data['y'] = savgol_filter(data['y'], 19, 1)
-
-    #velocity calculation, exclude velocities over 1000
-
-    # euclidean distance between successive coordinate samples
-    # no entry for first datapoint
-    velocities = (np.diff(data['x']) ** 2 + np.diff(data['y']) ** 2) ** 0.5
-
-    # convert from px/msec to deg/s
-    velocities *= px2deg * sampling_rate
-
-    # replace "too fast" velocities with previous velocity
-    accelerations = [float(0)]
-    filtered_velocities = [float(0)]
-    for vel in velocities:
-        # TODO make threshold a parameter
-        if vel > 1000:  # deg/s
-            # ignore very fast velocities
-            vel = filtered_velocities[-1]
-        # acceleration is change of velocities over the last msec
-        accelerations.append((vel - filtered_velocities[-1]) * sampling_rate)
-        filtered_velocities.append(vel)
-    # TODO report how often that happens
-
-    #save data to file
-    data=np.array([
-        filtered_velocities,
-        accelerations,
-        # TODO add time np.arange(len(filtered_velocities))
-        data['x'],
-        data['y']])
-
-    # TODO think about just saving it in binary form
-    np.savetxt(
-        outfile,
-        data.T,
-        fmt=['%f', '%f', '%f', '%f'],
-        delimiter='\t')
-
-if __name__ == '__main__':
-    px2deg = float(sys.argv[1])
-    infpath = sys.argv[2]
-    outfpath = sys.argv[3]
-    preproc(infpath, outfpath, px2deg)

code/tests/test_detect.py

@@ -0,0 +1,116 @@
+import pytest
+import numpy as np
+from . import utils as ut
+from .. import detect_events as d
+
+
+common_args = dict(
+    px2deg=0.01,
+    sampling_rate=1000.0,
+)
+
+
+def test_no_saccade():
+    samp = np.random.randn(1000)
+    data = ut.expand_samp(samp, y=0.0)
+    clf = d.EyegazeClassifier(**common_args)
+    p = clf.preproc(data, savgol_length=0.0, dilate_nan=0)
+    # the entire segment is labeled as a fixation
+    events = clf(p)
+    assert len(events) == 1
+    print(events)
+    assert events[0]['end_time'] - events[0]['start_time'] == 1.0
+    assert events[0]['label'] == 'FIXA'
+
+    # missing data split events
+    p[500:510]['x'] = np.nan
+    events = clf(p)
+    assert len(events) == 2
+    assert np.all([e['label'] == 'FIXA' for e in events])
+
+    # size doesn't matter
+    p[500:800]['x'] = np.nan
+    assert len(clf(p)) == len(events)
+
+
+def test_one_saccade():
+    samp = ut.mk_gaze_sample()
+
+    data = ut.expand_samp(samp, y=0.0)
+    clf = d.EyegazeClassifier(**common_args)
+    p = clf.preproc(data, dilate_nan=0)
+    events = clf(p)
+    assert events is not None
+    # we find at least the saccade
+    events = ut.events2df(events)
+    assert len(events) > 2
+    if len(events) == 4:
+        # full set
+        assert list(events['label']) == ['FIXA', 'ISAC', 'ILPS', 'FIXA'] or \
+            list(events['label']) == ['FIXA', 'ISAC', 'IHPS', 'FIXA']
+        for i in range(0, len(events) - 1):
+            # complete segmentation
+            assert events['start_time'][i + 1] == events['end_time'][i]
+
+
+def test_too_long_pso():
+    samp = ut.mk_gaze_sample(
+        pre_fix=1000,
+        post_fix=1000,
+        sacc=20,
+        sacc_dist=200,
+        # just under 30deg/s (max smooth pursuit)
+        pso=80,
+        pso_dist=100)
+    data = ut.expand_samp(samp, y=0.0)
+    clf = d.EyegazeClassifier(
+        max_initial_saccade_freq=.2,
+        **common_args)
+    p = clf.preproc(data, dilate_nan=0)
+    events = clf(p)
+    events = ut.events2df(events)
+    # there is no PSO detected
+    assert list(events['label']) == ['FIXA', 'SACC', 'FIXA']
+
+
+@pytest.mark.parametrize('infile', [
+    'inputs/raw_eyegaze/sub-32/beh/sub-32_task-movie_run-2_recording-eyegaze_physio.tsv.gz',
+    'inputs/raw_eyegaze/sub-09/ses-movie/func/sub-09_ses-movie_task-movie_run-2_recording-eyegaze_physio.tsv.gz',
+    'inputs/raw_eyegaze/sub-02/ses-movie/func/sub-02_ses-movie_task-movie_run-5_recording-eyegaze_physio.tsv.gz',
+])
+def test_real_data(infile):
+    data = np.recfromcsv(
+        infile,
+        delimiter='\t',
+        names=['x', 'y', 'pupil', 'frame'])
+
+    clf = d.EyegazeClassifier(
+        #px2deg=0.0185581232561,
+        px2deg=0.0266711972026,
+        sampling_rate=1000.0)
+    p = clf.preproc(data)
+
+    events = clf(
+        p[:50000],
+        #p,
+    )
+
+    evdf = ut.events2df(events)
+
+    labels = list(evdf['label'])
+    # find all kinds of events
+    for t in ('FIXA', 'PURS', 'SACC', 'LPSO', 'HPSO',
+              'ISAC', 'IHPS'):
+              # 'ILPS' one file doesn't have any
+        assert t in labels
+    return
+
+    ut.show_gaze(pp=p[:50000], events=events, px2deg=0.0185581232561)
+    #ut.show_gaze(pp=p, events=events, px2deg=0.0185581232561)
+    import pylab as pl
+    saccades = evdf[evdf['label'] == 'SACC']
+    isaccades = evdf[evdf['label'] == 'ISAC']
+    print('#saccades', len(saccades), len(isaccades))
+    pl.plot(saccades['amp'], saccades['peak_vel'], '.', alpha=.3)
+    pl.plot(isaccades['amp'], isaccades['peak_vel'], '.', alpha=.3)
+    pl.show()

code/tests/test_nystrom.py

@@ -0,0 +1,94 @@
+import numpy as np
+from . import utils as ut
+from .. import detect_events as d
+
+
+common_args = dict(
+    # we don't know what the stimulus props are
+    # variant1
+    #px2deg=d.deg_per_pixel(0.516, 0.6, 1024),
+    #sampling_rate=500.0,
+    # variant2
+    px2deg=d.deg_per_pixel(0.377, 0.67, 1024),
+    sampling_rate=1250.0,
+)
+
+
+def test_target_data():
+    label_remap = {
+        1: 'FIXA',
+        2: 'SACC',
+        3: 'PSO',
+    }
+    clf = d.EyegazeClassifier(**common_args)
+    data = np.recfromcsv(
+        'inputs/nystrom_target/1_2.csv',
+        usecols=[1, 2, 3, 4])
+    events = []
+    ev_type = None
+    ev_start = None
+    vels = []
+    for i in range(len(data)):
+        s = data[i]
+        if ev_type is None and s['event_type'] in (1, 2):
+            ev_type = s['event_type']
+            ev_start = i
+        elif ev_type is not None and s['event_type'] != ev_type:
+            amp, pv, medvel = clf._get_signal_props(data[ev_start:i])
+            events.append(dict(
+                id=len(events),
+                label=label_remap.get(ev_type),
+                start_time=0.0 if ev_start is None else
+                float(ev_start) / common_args['sampling_rate'],
+                end_time=float(i) / common_args['sampling_rate'],
+                peak_vel=pv,
+                amp=amp,
+            ))
+            vels = []
+            ev_type = s['event_type'] if s['event_type'] in (1, 2) else None
+            ev_start = i
+        if ev_type:
+            vels.append(s['vel'])
+    ut.show_gaze(pp=data, events=events, **common_args)
+    #for e in events:
+    #    print(e)
+    import pylab as pl
+    events = ut.events2df(events)
+    saccades = events[events['label'] == 'SACC']
+    isaccades = events[events['label'] == 'ISAC']
+    print('#saccades', len(saccades), len(isaccades))
+    pl.plot(saccades['amp'], saccades['peak_vel'], '.', alpha=.3)
+    pl.plot(isaccades['amp'], isaccades['peak_vel'], '.', alpha=.3)
+    pl.show()
+
+def test_real_data():
+    data = np.recfromcsv(
+        'inputs/event_detector_1.1/1_2.csv',
+        usecols=[0, 1])
+    # when both coords are zero -> missing data
+    data[np.logical_and(data['x'] == 0, data['y'] == 0)] = (np.nan, np.nan)
+
+    clf = d.EyegazeClassifier(
+        min_intersaccade_duration=0.04,
+        # high threshold, static stimuli, should not have pursuit
+        max_fixation_amp=4.0,
+        **common_args)
+    p = clf.preproc(data, dilate_nan=0.03)
+
+    events = clf(p)
+
+    # TODO compare against output from original matlab code
+    #return
+    for e in events:
+        print('{:.4f} -> {:.4f}: {} ({})'.format(
+            e['start_time'], e['end_time'], e['label'], e['id']))
+
+    ut.show_gaze(pp=p, events=events, **common_args)
+    import pylab as pl
+    events = ut.events2df(events)
+    saccades = events[events['label'] == 'SACC']
+    isaccades = events[events['label'] == 'ISAC']
+    print('#saccades', len(saccades), len(isaccades))
+    pl.plot(saccades['amp'], saccades['peak_vel'], '.', alpha=.3)
+    pl.plot(isaccades['amp'], isaccades['peak_vel'], '.', alpha=.3)
+    pl.show()

code/tests/test_preproc.py

@@ -0,0 +1,93 @@
+import numpy as np
+from . import utils as ut
+from .. import detect_events as d
+
+
+common_args = dict(
+    px2deg=0.0185581232561,
+    sampling_rate=1000.0,
+)
+
+
+def test_px2deg():
+    assert (
+        d.deg_per_pixel(26.5, 63, 1280) -
+        # value from paper
+        0.0185546875) < 0.0001
+
+
+def test_spike_filter():
+    samp = np.random.randn(1000)
+    data = ut.expand_samp(samp, y=0.0)
+    p = d.filter_spikes(data.copy())
+    assert np.std(data['x']) > np.std(p['x'])
+    assert data['x'][0] == p['x'][0]
+    assert data['x'][-1] == p['x'][-1]
+
+
+def test_preproc():
+    samp = np.random.randn(1000)
+    data = ut.expand_samp(samp, y=0.0)
+    clf = d.EyegazeClassifier(**common_args)
+    p = clf.preproc(data.copy(), savgol_length=0.019, savgol_polyord=1)
+    # first values are always zero
+    assert p[0]['vel'] == 0
+    assert p[0]['accel'] == 0
+    p = p['x']
+    # shorter filter leaves more "noise"
+    p_linshort = clf.preproc(
+        data.copy(), savgol_length=0.009, savgol_polyord=1)['x']
+    assert np.std(p) < np.std(p_linshort)
+    # more flexible filter leaves more "noise"
+    p_quad = clf.preproc(
+        data.copy(), savgol_length=0.019, savgol_polyord=2)['x']
+    assert np.std(p) < np.std(p_quad)
+
+    # insert small NaN patch
+    data['x'][100:110] = np.nan
+    assert np.sum(np.isnan(data['x'])) == 10
+    p = clf.preproc(
+        data.copy(), savgol_length=0.019, savgol_polyord=1,
+        min_blink_duration=10.0)['x']
+    # the original data does NOT change!
+    assert np.sum(np.isnan(data['x'])) == 10
+    # the gap will widen
+    assert np.sum(np.isnan(p)) == 28
+    # a wider filter will increase the gap, actual impact depends on
+    # filter setup
+    p = clf.preproc(
+        data.copy(), savgol_length=0.101, savgol_polyord=1,
+        min_blink_duration=10.0)['x']
+    assert np.sum(np.isnan(p)) > 28
+    # no widen the gap pre filtering (disable filter to test that)
+    p = clf.preproc(
+        data.copy(), savgol_length=0.001, savgol_polyord=0,
+        min_blink_duration=0.0, dilate_nan=0.015)['x']
+    # the original data still does NOT change!
+    assert np.sum(np.isnan(data['x'])) == 10
+    # the gap will widen
+    assert np.sum(np.isnan(p)) == 10 + 2 * 15
+
+    # insert another small gap that we do not want to widen
+    data['x'][200:202] = np.nan
+    assert np.sum(np.isnan(data['x'])) == 12
+    p = clf.preproc(
+        data.copy(), savgol_length=0.001, savgol_polyord=0,
+        min_blink_duration=0.008, dilate_nan=0.015)['x']
+    assert np.sum(np.isnan(p)) == 10 + 2 * 15 + 2
+
+    samp = [0.0, 2.0]
+    data = ut.expand_samp(samp, y=0.0)
+    clf = d.EyegazeClassifier(px2deg=1.0, sampling_rate=10.0)
+    p = clf.preproc(
+        data.copy(), savgol_length=0, dilate_nan=0,
+        median_filter_length=0)
+    # 2 deg in 0.1s -> 20deg/s
+    assert p['vel'][-1] == 20
+    assert p['accel'][-1] == 200
+    assert 'med_vel' not in p.dtype.names
+
+    data['x'][1] = 200
+    p = clf.preproc(data.copy(), savgol_length=0, dilate_nan=0)
+    assert p['vel'][-1] == 0
+    assert p['accel'][-1] == 0

code/tests/utils.py

@@ -0,0 +1,132 @@
+import numpy as np
+import os
+
+import logging
+lgr = logging.getLogger('studyforrest.utils')
+
+
+if 'NOISE_SEED' in os.environ:
+    seed = int(os.environ['NOISE_SEED'])
+else:
+    seed = np.random.randint(100000000)
+    lgr.warn('RANDOM SEED: %i', seed)
+np.random.seed(seed)
+
+
+def get_noise(size, loc, std):
+    noise = np.random.randn(size)
+    noise *= std
+    noise += loc
+    return noise
+
+
+def get_drift(size, start, dist):
+    return np.linspace(start, start + dist, size)
+
+
+def mk_gaze_sample(
+        pre_fix=1000,
+        post_fix=1000,
+        fix_std=5,
+        sacc=20,
+        sacc_dist=200,
+        pso=30,
+        pso_dist=-40,
+        start_x=0.0,
+        noise_std=2,
+        ):
+    duration = pre_fix + sacc + pso + post_fix
+    samp = np.empty(duration)
+    # pre_fix
+    t = 0
+    pos = start_x
+    samp[t:t + pre_fix] = get_noise(pre_fix, pos, fix_std)
+    t += pre_fix
+    # saccade
+    samp[t:t + sacc] = get_drift(sacc, pos, sacc_dist)
+    t += sacc
+    pos += sacc_dist
+    # pso
+    samp[t:t + pso] = get_drift(pso, pos, pso_dist)
+    t += pso
+    pos += pso_dist
+    # post fixation
+    samp[t:t + post_fix] = get_noise(post_fix, pos, fix_std)
+    samp += get_noise(len(samp), 0, noise_std)
+
+    return samp
+
+
+def expand_samp(samp, y=1000.0):
+    n = len(samp)
+    return np.core.records.fromarrays([
+        samp,
+        [y] * n,
+        [0.0] * n,
+        [0] * n],
+        names=['x', 'y', 'pupil', 'frame'])
+
+
+def samp2file(data, fname):
+    np.savetxt(
+        fname,
+        data.T,
+        fmt=['%.1f', '%.1f', '%.1f', '%i'],
+        delimiter='\t')
+
+
+def show_gaze(data=None, pp=None, events=None, px2deg=None, sampling_rate=1000.0):
+    colors = {
+        'FIXA': 'gray',
+        'PURS': 'red',
+        'SACC': 'green',
+        'ISAC': 'pink',
+        'HPSO': 'yellow',
+        'IHPS': 'orange',
+        'LPSO': 'cyan',
+        'ILPS': 'blue',
+    }
+
+    import pylab as pl
+    if data is not None:
+        pl.plot(
+            np.linspace(0, len(data) / sampling_rate, len(data)),
+            data['x'],
+            color='blue')
+        pl.plot(
+            np.linspace(0, len(data) / sampling_rate, len(data)),
+            data['y'],
+            color='blue')
+    if pp is not None:
+        pl.plot(
+            np.linspace(0, len(pp) / sampling_rate, len(pp)),
+            pp['vel'],
+            #(pp['accel'] / np.abs(pp['accel'][~np.isnan(pp['accel'])]).max()) * 1000,
+            #(pp['accel'] / np.abs(pp['accel']).max()) * 1000,
+            color='gray')
+        pl.plot(
+            np.linspace(0, len(pp) / sampling_rate, len(pp)),
+            pp['x'],
+            color='orange')
+        pl.plot(
+            np.linspace(0, len(pp) / sampling_rate, len(pp)),
+            pp['y'],
+            color='orange')
+        #pl.plot(
+        #    np.linspace(0, len(pp) / sampling_rate, len(pp)),
+        #    pp['med_vel'],
+        #    color='black')
+    if events is not None:
+        for ev in events:
+            pl.axvspan(
+                ev['start_time'],
+                ev['end_time'],
+                color=colors[ev['label']],
+                alpha=0.3)
+            pl.text(ev['start_time'], 0, '{:.1f}'.format(ev['id']), color='red')
+    pl.show()
+
+
+def events2df(events):
+    import pandas as pd
+    return pd.DataFrame(events)