2021-07-11 15:39:28 +00:00 · 2021-07-11 13:05:56 +00:00
5 changed files with 166 additions and 160 deletions
--- a/43
+++ b/43
@ -1,18 +1,37 @@
+# use `chronic` to make output look neater, if available
+CHRONIC=$(shell which chronic || echo '' )
+
+PYTHON=python
+
+
 all: main.pdf

-main.pdf: main.tex references.bib results_def.tex figures
-	latexmk -pdf -g $<
-
-results_def.tex: code/mk_figuresnstats.py
-	bash -c 'set -o pipefail; code/mk_figuresnstats.py -s | tee results_def.tex'
-
-figures: figures-stamp
-
-figures-stamp: code/mk_figuresnstats.py
-	code/mk_figuresnstats.py -f -r -m
+# important to process stats and figures first, such that
+# up-to-date versions are compiled into the manuscript
+main.pdf: main.tex results_def.tex references.bib 
+	@echo "# Render figures"
 	$(MAKE) -C img
-	touch $@
+	@echo "# Render manuscript"
+	@$(CHRONIC) latexmk -pdf -g $<
+
+# the stats-script outputs all scores and figures
+results_def.tex: code/mk_figuresnstats.py
+	@test -z "$$VIRTUAL_ENV" && \
+		echo "ERROR: must be executed in a virtual env (set VIRTUAL_ENV to fake one)" && \
+		exit 1 || true
+	@echo "# Ensure REMODNAV installation"
+	@python -m pip install pandas seaborn sklearn datalad
+	@datalad get -n remodnav
+	@$(CHRONIC) pip install -e remodnav
+	@rm -f $@
+	@REMODNAV_RESULTS=$@ $(PYTHON) code/mk_figuresnstats.py -s -f -r -m

 clean:
-	rm -f main.bbl main.aux main.blg main.log main.out main.pdf main.tdo main.fls main.fdb_latexmk example.eps img/*eps-converted-to.pdf texput.log results_def.tex figures-stamp
+	rm -f main.bbl main.aux main.blg main.log main.out main.pdf main.tdo \
+		main.fls main.fdb_latexmk texput.log \
+		results_def.tex
 	$(MAKE) -C img clean
+
+virtualenv:
+
+.PHONY: clean
--- a/README.md
+++ b/README.md
@ -6,35 +6,28 @@ This repository contains the raw data, the code to generate summary statistics,

 To recompute results and compile the paper, do the following:

-[Optional] create a virtual environment:
+- Create a [virtual environment](https://docs.python.org/3/tutorial/venv.html) and activate it:

-    # create and enter a new virtual environment (optional)
+```
+    # one way to create a virtual environment:
    virtualenv --python=python3 ~/env/remodnav
    . ~/env/remodnav/bin/activate
+```
 
- if you haven't yet, install [``remodnav``](https://github.com/psychoinformatics-de/remodnav), ``seaborn``, and
- [``datalad``](https://www.datalad.org). Depending on your operating system, datalad can be installed via
- ``pip install datalad`` or ``sudo apt-get install datalad`` (please check the 
- [docs](http://docs.datalad.org/en/latest/gettingstarted.html) if you are unsure which option is applicable to your system)
+- ``clone`` the repository with ``git clone https://github.com/psychoinformatics-de/paper-remodnav.git``
+- Navigate into the repository and run ``make``

-Install from [PyPi](https://pypi.org/project/remodnav):
-
-    # install from PyPi
-    pip install remodnav seaborn sklearn
-    # if not installed with another method
-    pip install datalad
-
- ``datalad clone`` the repository with ``datalad clone https://github.com/psychoinformatics-de/paper-remodnav.git``
-
- Appropriate Makefiles within the directory will execute data retrieval via datalad (about 550MB in total),
+Appropriate Makefiles within the directory will install necessary Python requirements (the ``remodnav`` Python package, ``datalad``, ``pandas``, ``seaborn``, and ``sklearn``), execute data retrieval via [DataLad](http://datalad.org) (about 550MB in total),
 compute the results and figures from ``code/mk_figuresnstats.py``, insert the results and rendered figures in the
-main.tex file, and render the PDF with a single call from the root of the directory: ``make``
-
- Note that [inkscape](https://inkscape.org/de/release/inkscape-0.92.4/), [latexmk](https://mg.readthedocs.io/latexmk.html),
-  and [texlive-latex-extra](https://wiki.ubuntuusers.de/TeX_Live/) need to be installed on your system to render the figures and the     PDF.
-
+main.tex file, and render the PDF.
 The full PDF will be ``main.pdf``.

+## Software requirements
+
+Note that [inkscape](https://inkscape.org/de/release/inkscape-0.92.4/), [latexmk](https://mg.readthedocs.io/latexmk.html),
+  and [texlive-latex-extra](https://wiki.ubuntuusers.de/TeX_Live/) need to be installed on your system to render the figures and the PDF.
+
+## Getting help

 If you encounter failures, e.g. due to uninstalled python modules, restart ``make`` after running ``make clean``.
 If you encounter failures you suspect are due to deficiencies in this repository, please submit an
--- a/code/mk_figuresnstats.py
+++ b/code/mk_figuresnstats.py
@ -1,22 +1,38 @@
 #!/usr/bin/env python

-import os.path as op
-import itertools
-import numpy as np
-import pylab as pl
-import seaborn as sns
-from remodnav import EyegazeClassifier
+import argparse
+from collections import OrderedDict
+from copy import deepcopy
 from glob import glob
-import datalad.api as dl
-#from remodnav.tests.test_labeled import load_data as load_anderson
-
-
-def load_anderson(category, name):
-    from scipy.io import loadmat
-    from datalad.api import get
-    from remodnav import clf as CLF
+import itertools
 import os.path as op
+from os import environ
+import sys

+import matplotlib.pyplot as plt
+from matplotlib.lines import Line2D
+import numpy as np
+import pandas as pd
+from scipy.signal import (
+    butter,
+    filtfilt,
+)
+from scipy.io import loadmat
+from scipy.spatial import distance
+import seaborn as sns
+from sklearn.metrics import cohen_kappa_score
+
+from datalad.api import get as datalad_get
+
+from remodnav import (
+    EyegazeClassifier,
+    clf as CLF,
+)
+from remodnav.tests import utils as ut
+
+
+#from remodnav.tests.test_labeled import load_data as load_anderson
+def load_anderson(category, name):
    fname = op.join(*(
        ('remodnav', 'remodnav', 'tests', 'data', 'anderson_etal',
         'annotated_data') + \
@ -26,7 +42,7 @@ def load_anderson(category, name):
        ) + \
        (name + ('' if name.endswith('.mat') else '.mat'),))
    )
-    get(fname)
+    datalad_get(fname)
    m = loadmat(fname)
    # viewing distance
    vdist = m['ETdata']['viewDist'][0][0][0][0]
@ -258,7 +274,7 @@ def confusion(refcoder,
    # initialize a maximum misclassification rate, to later automatically reference,
    max_mclf = 0
    # coders are in axis labels too
-    #pl.suptitle('Jaccard index for movement class labeling {} vs. {}'.format(
+    #plt.suptitle('Jaccard index for movement class labeling {} vs. {}'.format(
    #    refcoder, coder))
    for stimtype, stimlabel in (
            ('img', 'Images'),
@ -298,11 +314,11 @@ def confusion(refcoder,

            nlabels = [len(l) for l in labels]
            if len(np.unique(nlabels)) > 1:
-                print(
+                rsout(
                    "% #\n% # %INCONSISTENCY Found label length mismatch "
                    "between coders ({}, {}) for: {}\n% #\n".format(
                        refcoder, coder, fname))
-                print('% Truncate labels to shorter sample: {}'.format(
+                rsout('% Truncate labels to shorter sample: {}'.format(
                    nlabels))
                order_idx = np.array(nlabels).argsort()
                labels[order_idx[1]] = \
@ -329,7 +345,7 @@ def confusion(refcoder,
        # zero out diagonal for bandwidth
        conf *= ((np.eye(len(conditions)) - 1) * -1)
        if figures:
-            pl.subplot(1, 3, plotter)
+            plt.subplot(1, 3, plotter)
            sns.heatmap(
                #(conf / nsamples) * 100,
                jinter / junion,
@ -341,14 +357,14 @@ def confusion(refcoder,
                vmin=0.0,
                vmax=1.0,
            )
-            pl.xlabel('{} labeling'.format(refcoder))
-            pl.ylabel('{} labeling'.format(coder))
+            plt.xlabel('{} labeling'.format(refcoder))
+            plt.ylabel('{} labeling'.format(coder))
            # stats are given proper below
-            #pl.title('"{}" (glob. misclf-rate): {:.1f}% (w/o pursuit: {:.1f}%)'.format(
+            #plt.title('"{}" (glob. misclf-rate): {:.1f}% (w/o pursuit: {:.1f}%)'.format(
            #    stimtype,
            #    (np.sum(conf) / nsamples) * 100,
            #    (np.sum(conf[:3, :3]) / nsamples_nopurs) * 100))
-            pl.title(stimlabel)
+            plt.title(stimlabel)
            plotter += 1
        msclf_refcoder = dict(zip(conditions, conf.sum(axis=1)/conf.sum() * 100))
        msclf_coder = dict(zip(conditions, conf.sum(axis=0)/conf.sum() * 100))
@ -368,7 +384,7 @@ def confusion(refcoder,
                    ('SACcod', '%.0f', msclf_coder['SAC']),
                    ('PSOcod', '%.0f', msclf_coder['PSO']),
                    ('SPcod', '%.0f', msclf_coder['PUR'])):
-                print('\\newcommand{\\%s%s}{%s}'
+                rsout('\\newcommand{\\%s%s}{%s}'
                      % (label_prefix, key, format % value))
                # update classification performance only if there sth worse
                if (np.sum(conf[:3, :3]) / nsamples_nopurs * 100) > max_mclf:
@ -376,10 +392,10 @@ def confusion(refcoder,
            # print original outputs, but make them LaTeX-safe with '%'. This
            # should make it easier to check correct placements of stats in the
            # table
-            print('% ### {}'.format(stimtype))
-            print('% Comparison | MCLF | MCLFw/oP | Method | Fix | Sacc | PSO | SP')
-            print('% --- | --- | --- | --- | --- | --- | --- | ---')
-            print('% {} v {} | {:.1f} | {:.1f} | {} | {:.0f} | {:.0f} | {:.0f} | {:.0f}'.format(
+            rsout('% ### {}'.format(stimtype))
+            rsout('% Comparison | MCLF | MCLFw/oP | Method | Fix | Sacc | PSO | SP')
+            rsout('% --- | --- | --- | --- | --- | --- | --- | ---')
+            rsout('% {} v {} | {:.1f} | {:.1f} | {} | {:.0f} | {:.0f} | {:.0f} | {:.0f}'.format(
                refcoder,
                coder,
                (np.sum(conf) / nsamples) * 100,
@ -390,7 +406,7 @@ def confusion(refcoder,
                msclf_refcoder['PSO'],
                msclf_refcoder['PUR'],
            ))
-            print('% -- | --  | -- | {} | {:.0f} | {:.0f} | {:.0f} | {:.0f}'.format(
+            rsout('% -- | --  | -- | {} | {:.0f} | {:.0f} | {:.0f} | {:.0f}'.format(
                coder,
                msclf_coder['FIX'],
                msclf_coder['SAC'],
@ -400,14 +416,13 @@ def confusion(refcoder,
    return max_mclf


-def savefigs(fig,
-             stat):
+def mk_confusion_figures(fig, stat):
    """
    small helper function to save all confusion matrices
    """
    max_mclf = 0
    for pair in itertools.combinations(['MN', 'RA', 'AL'], 2):
-        pl.figure(
+        plt.figure(
            # fake size to get the font size down in relation
            figsize=(14, 3),
            dpi=120,
@ -416,15 +431,15 @@ def savefigs(fig,
                                 pair[1],
                                 fig,
                                 stat)
-        pl.savefig(
+        plt.savefig(
            op.join('img', 'confusion_{}_{}.svg'.format(*pair)),
            transparent=True,
            bbox_inches="tight")
-        pl.close()
+        plt.close()
        if cur_max_mclf > max_mclf:
            max_mclf = cur_max_mclf
    if stat:
-        print('\\newcommand{\\maxmclf}{%s}'
+        rsout('\\newcommand{\\maxmclf}{%s}'
              % ('%.1f' % max_mclf))


@ -441,8 +456,6 @@ def quality_stats():
    list of command invocations if the script is ran from the command line at the
    end of the script.
    """
-    import matplotlib.pyplot as plt
-
    datapath_mri = op.join('data', 'raw_eyegaze', 'sub-*', 'ses-movie', 'func',
                           'sub-*_ses-movie_task-movie_run-*_recording-eyegaze_physio.tsv.gz')
    datapath_lab = op.join('data', 'raw_eyegaze', 'sub-*', 'beh',
@ -452,7 +465,7 @@ def quality_stats():
                          (datapath_mri, 'mri')]:
        infiles = glob(data)
        for f in infiles:
-            dl.get(f)
+            datalad_get(f)
        # make sure we have 15 subjects' data
        assert len(infiles) == 120
        print("Currently processing data from {} sample".format(assoc))
@ -478,7 +491,7 @@ def quality_stats():
        loss = np.nanmean(losses)
        # print results as Latex command using 'assoc' as sample identifier in name
        label_loss = 'avgloss{}'.format(assoc)
-        print('\\newcommand{\\%s}{%s}'
+        rsout('\\newcommand{\\%s}{%s}'
              % (label_loss, loss))
        # vels is a list of arrays atm
        v = np.concatenate(vels).ravel()
@ -586,9 +599,6 @@ def S2SRMS():
        https://doi.org/10.1038/sdata.2016.92

    """
-    from scipy.spatial import distance
-    import datalad.api as dl
-
    # globs for all data for MRI and Lab
    datapath_mri = op.join('data', 'raw_eyegaze', 'sub-*', 'ses-movie', 'func',
                           'sub-*_ses-movie_task-movie_run-*_recording-eyegaze_physio.tsv.gz')
@ -609,7 +619,7 @@ def S2SRMS():
        window = 1000
        median_distances = []
        for f in infiles:
-            dl.get(f)
+            datalad_get(f)
            data = np.genfromtxt(f,
                                  delimiter='\t',
                                  usecols=(0, 1) # get only x and y column
@ -632,7 +642,7 @@ def S2SRMS():
        meanRMS = np.nanmean(median_distances)
        # print results as Latex command using 'assoc' as sample identifier in name
        label_RMS = 'RMS{}'.format(assoc)
-        print('\\newcommand{\\%s}{%s}'
+        rsout('\\newcommand{\\%s}{%s}'
              % (label_RMS, meanRMS))
        # save the results in variables
        if assoc == 'lab':
@ -646,9 +656,6 @@ def flowchart_figs():
    Just for future reference: This is the subset of preprocessed and raw data
    used for the flowchart of the algorithm. Not to be executed.
    """
-    import matplotlib.pyplot as plt
-    from scipy import signal
-
    datapath = op.join('data', 'raw_eyegaze', 'sub-32', 'beh',
                        'sub-32_task-movie_run-1_recording-eyegaze_physio.tsv.gz')
    data = np.recfromcsv(datapath,
@ -690,7 +697,7 @@ def flowchart_figs():
    def _butter_lowpass(cutoff, fs, order=5):
        nyq = 0.5 * fs
        normal_cutoff = cutoff / nyq
-        b, a = signal.butter(
+        b, a = butter(
            order,
            normal_cutoff,
            btype='low',
@ -703,8 +710,8 @@ def flowchart_figs():
    # let's get a data sample with no saccade
    win_data = p[16600:17000]
    b, a = _butter_lowpass(lp_cutoff_freq, sr)
-    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['x'] = filtfilt(b, a, win_data['x'], method='gust')
+    win_data['y'] = filtfilt(b, a, win_data['y'], method='gust')

    filtered_vels = cal_velocities(data=win_data, sr=1000, px2deg=0.0266711972026)
    fig, ax1 = plt.subplots()
@ -727,14 +734,14 @@ def cal_velocities(data, sr, px2deg):
    return velocities


-def plot_raw_vel_trace():
+def mk_raw_vel_trace_figures():
    """
    Small helper function to plot raw velocity traces, as requested by reviewer 2
    in the second revision.
    """
-    import matplotlib.pyplot as plt
-    # use the same data as in savegaze() (no need for file retrieval, should be there)
-    dl.install(op.join('data', 'raw_eyegaze'))
+    # use the same data as in mk_eyegaze_classification_figures()
+    # (no need for file retrieval, should be there)
+    datalad_get(op.join('data', 'raw_eyegaze'), get_data=False)
    infiles = [
        op.join(
            'data',
@ -751,7 +758,7 @@ def plot_raw_vel_trace():
    # load data
    for i, f in enumerate(infiles):
        # read data
-        dl.get(f)
+        datalad_get(f)
        data = np.recfromcsv(f,
                             delimiter='\t',
                             names=['x', 'y', 'pupil', 'frame'])
@ -798,20 +805,17 @@ def plot_raw_vel_trace():
        ax2.plot(time_idx,
            velocities,
            color=vel_color, lw=1)
-        pl.savefig(
+        plt.savefig(
            op.join('img', 'rawtrace_{}.svg'.format(ext)),
            transparent=True,
            bbox_inches="tight")
-        pl.close()
+        plt.close()


-def savegaze():
+def mk_eyegaze_classification_figures():
    """
    small function to generate and save remodnav classification figures
    """
-    from remodnav.tests import utils as ut
-    import pylab as pl
-
    # use two examplary files (lab + MRI) used during testing as well
    # hardcoding those, as I see no reason for updating them
    infiles = [
@ -827,7 +831,7 @@ def savegaze():
    ]
    # one call per file due to https://github.com/datalad/datalad/issues/3356
    for f in infiles:
-        dl.get(f)
+        datalad_get(f)
    for f in infiles:
        # read data
        data = np.recfromcsv(f,
@ -846,11 +850,11 @@ def savegaze():
        # for both data types (lab & mri)
        events = clf(p[15000:25000])
        # we remove plotting of details in favor of plotting raw gaze and
-        # velocity traces with plot_raw_vel_trace() as requested by reviewer 2
+        # velocity traces with mk_raw_vel_trace_figures() as requested by reviewer 2
        # in the second round of revision
        #events_detail = clf(p[24500:24750])

-        fig = pl.figure(
+        fig = plt.figure(
            # fake size to get the font size down in relation
            figsize=(14, 2),
            dpi=120,
@ -861,14 +865,14 @@ def savegaze():
            sampling_rate=1000.0,
            show_vels=True,
            coord_lim=(0, 1280),
-            vel_lim=(0, 1000))
-        pl.savefig(
+            vel_lim=(0.001, 1000))
+        plt.savefig(
            op.join('img', 'remodnav_{}.svg'.format(ext)),
            transparent=True,
            bbox_inches="tight")
-        pl.close()
+        plt.close()
        # plot details
-        fig = pl.figure(
+        fig = plt.figure(
            # fake size to get the font size down in relation
            figsize=(7, 2),
            dpi=120,
@ -880,21 +884,17 @@ def savegaze():
        #    show_vels=True,
        #    coord_lim=(0, 1280),
        #    vel_lim=(0, 1000))
-        #pl.savefig(
+        #plt.savefig(
        #    op.join('img', 'remodnav_{}_detail.svg'.format(ext)),
        #    transparent=True,
        #    bbox_inches="tight")
-        #pl.close()
+        #plt.close()


-def mainseq(s_mri,
-            s_lab):
+def mk_mainseq_figures(s_mri, s_lab):
    """
    plot main sequences from movie data for lab and mri subjects.
    """
-    import pandas as pd
-    from matplotlib.lines import Line2D
-
    datapath = op.join('data',
                       'studyforrest-data-eyemovementlabels',
                       'sub*',
@ -904,8 +904,7 @@ def mainseq(s_mri,
                       # while the visible content hardly changes
                       '*run-2*.tsv')
    data = sorted(glob(datapath))
-    from datalad.api import get
-    get(dataset='.', path=data)
+    datalad_get(path=data)

    # create dataframes for mri and lab subjects to plot in separate plots
    for (ids, select_sub, ext) in [
@ -934,7 +933,7 @@ def mainseq(s_mri,
            SACCs = d[(d.label == 'SACC') | (d.label == 'ISAC')]
            PSOs = d[(d.label == 'HPSO') | (d.label == 'IHPS') | (d.label == 'LPSO') | (d.label == 'ILPS')]

-            fig = pl.figure(
+            fig = plt.figure(
                # fake size to get the font size down in relation
                figsize=(6, 4),
                dpi=120,
@ -944,7 +943,7 @@ def mainseq(s_mri,
                    (SACCs, '.', 'red'),
                    (PSOs, '+', 'darkblue'),
                    ):
-                pl.loglog(
+                plt.loglog(
                    ev['amp'],
                    ev['peak_vel'],
                    sym,
@ -972,12 +971,12 @@ def mainseq(s_mri,
                       markersize=10),
            ]

-            pl.ylim((10.0, 1000))
-            pl.xlim((0.01, 40.0))
-            pl.legend(handles=custom_legend, loc=4)
-            pl.ylabel('peak velocities (deg/s)')
-            pl.xlabel('amplitude (deg)')
-            pl.savefig(
+            plt.ylim((10.0, 1000))
+            plt.xlim((0.01, 40.0))
+            plt.legend(handles=custom_legend, loc=4)
+            plt.ylabel('peak velocities (deg/s)')
+            plt.xlabel('amplitude (deg)')
+            plt.savefig(
                op.join(
                    'img',
                    'mainseq{}_{}.svg'.format(
@ -985,7 +984,7 @@ def mainseq(s_mri,
                        ext)),
                transparent=True,
                bbox_inches="tight")
-            pl.close()
+            plt.close()


 def RMSD(mn,
@ -1058,7 +1057,6 @@ def get_remodnav_params(stim_type):
    for ev in events:
        ev['label'] = label_map[ev['label']]

-    from collections import OrderedDict
    durs = OrderedDict()
    durs['event']=[]
    durs['alg']=[]
@ -1083,7 +1081,6 @@ def print_RMSD():
    for use in main.tex.
    """
    # I don't want to overwrite the original dicts
-    from copy import deepcopy
    img = deepcopy(image_params)
    dots = deepcopy(dots_params)
    video = deepcopy(video_params)
@ -1107,7 +1104,7 @@ def print_RMSD():
                    label_prefix = '{}{}{}{}'.format(ev, stim, par, alg)
                    # take the value of the event and param type by indexing the dict with the position of
                    # the current algorithm
-                    print('\\newcommand{\\%s}{%s}'
+                    rsout('\\newcommand{\\%s}{%s}'
                          %(label_prefix, dic[0][ev][par][dic[0][ev]['alg'].index(alg)]))
        # compute RMSDs for every stimulus category
        for ev in event_types:
@ -1118,28 +1115,26 @@ def print_RMSD():
            algo = dic[0][ev]['alg']
            for i in range(len(rmsd)):
                label = 'rank{}{}{}'.format(ev, stim, algo[i])
-                print('\\newcommand{\\%s}{%s}'
+                rsout('\\newcommand{\\%s}{%s}'
                      %(label, rmsd[i]))


-def plot_dist(figures):
+def mk_event_duration_histograms(figures):
    """
    Plot the events duration distribution per movie run, per data set.
    """
-    import pandas as pd
-
    # do nothing if we don't want to plot
    if not figures:
        return

-    dl.install(op.join('data', 'studyforrest-data-eyemovementlabels'))
+    datalad_get(op.join('data', 'studyforrest-data-eyemovementlabels'))
    datapath = op.join('data',
                       'studyforrest-data-eyemovementlabels',
                       'sub*',
                       '*.tsv')

    data = sorted(glob(datapath))
-    dl.get(dataset='.', path=data)
+    datalad_get(path=data, get_data=False)

    for ds, ds_name in [(mri_ids, 'mri'), (lab_ids, 'lab')]:
        dfs = [
@ -1161,16 +1156,16 @@ def plot_dist(figures):
                (FIX, 'fixation', (0, 1.0), (1, 50000)),
                (PSOs, 'PSO', (0, 0.04), (1, 26000)),
                (PURs, 'pursuit', (0, .8), (1, 30000))]:
-            fig = pl.figure(figsize=(3,2))
-            pl.hist(ev_df['duration'].values,
+            fig = plt.figure(figsize=(3,2))
+            plt.hist(ev_df['duration'].values,
                    bins='doane',
                    range=x_lim,
                    color='gray')
                    #log=True)
-            pl.xlabel('{} duration in s'.format(label))
-            pl.xlim(x_lim)
-            pl.ylim(y_lim)
-            pl.savefig(
+            plt.xlabel('{} duration in s'.format(label))
+            plt.xlim(x_lim)
+            plt.ylim(y_lim)
+            plt.savefig(
                op.join(
                    'img',
                    'hist_{}_{}.svg'.format(
@ -1178,7 +1173,7 @@ def plot_dist(figures):
                        ds_name)),
                transparent=True,
                bbox_inches="tight")
-            pl.close()
+            plt.close()


 def kappa():
@ -1189,7 +1184,6 @@ def kappa():
    """
    px2deg = None
    sr = None
-    from sklearn.metrics import cohen_kappa_score
    # for every stimulus type
    for stim in ['img', 'dots', 'video']:
        # for every eye movement label used in Anderson et al. (2017)
@ -1229,11 +1223,11 @@ def kappa():
                        AL_res.append(labels)

                if len(MN_res[idx]) != len(RA_res[idx]):
-                    print(
+                    rsout(
                        "% #\n% # %INCONSISTENCY Found label length mismatch "
                        "between coders for: {}\n% #\n".format(fname))
                    shorter = min([len(RA_res[idx]), len(MN_res[idx])])
-                    print('% Truncate labels to shorter sample: {}'.format(
+                    rsout('% Truncate labels to shorter sample: {}'.format(
                        shorter))
                    # truncate the labels by indexing up to the highest index
                    # in the shorter list of labels
@ -1246,7 +1240,7 @@ def kappa():
            RA_res_flat = [item for sublist in RA_res for item in sublist]
            MN_res_flat = [item for sublist in MN_res for item in sublist]
            AL_res_flat = [item for sublist in AL_res for item in sublist]
-            #print(sum(RA_res_flat), sum(MN_res_flat))
+            #rsout(sum(RA_res_flat), sum(MN_res_flat))
            assert len(RA_res_flat) == len(MN_res_flat) == len(AL_res_flat)
            # compute Cohens Kappa
            for rating, comb in [('RAMN', [RA_res_flat, MN_res_flat]),
@ -1254,13 +1248,16 @@ def kappa():
                                 ('ALMN', [MN_res_flat, AL_res_flat])]:
                kappa = cohen_kappa_score(comb[0], comb[1])
                label = 'kappa{}{}{}'.format(rating, stim, ev)
-                print('\\newcommand{\\%s}{%s}' % (label, '%.2f' % kappa))
+                rsout('\\newcommand{\\%s}{%s}' % (label, '%.2f' % kappa))
+
+
+def rsout(str):
+    fname = environ.get('REMODNAV_RESULTS', None)
+    fobj = open(fname, 'a') if fname else sys.stdout
+    print(str, file=fobj)


 if __name__ == '__main__':
-
-    import argparse
-
    parser = argparse.ArgumentParser()
    parser.add_argument(
        '-f', '--figure', help='if given, figures will be produced.',
@ -1289,12 +1286,19 @@ if __name__ == '__main__':
    args = parser.parse_args()
    # generate & save figures; export the stats
    if args.figure or args.stats:
-        savefigs(args.figure, args.stats)
+        print("#\n# Render confusion matrix figures")
+        mk_confusion_figures(args.figure, args.stats)
+        print("#\n# Compute RMSD table values")
        print_RMSD()
-        plot_dist(args.figure)
+        print('#\n# Render event duration histograms')
+        mk_event_duration_histograms(args.figure)
+        print("#\n# Compute kappa score for inter-rater agreements")
        kappa()
-        plot_raw_vel_trace()
+        print('#\n# Render raw velocity traces')
+        mk_raw_vel_trace_figures()
    if args.mainseq:
-        mainseq(args.submri, args.sublab)
+        print('#\n# Render main sequence plots')
+        mk_mainseq_figures(args.submri, args.sublab)
    if args.remodnav:
-        savegaze()
+        print('#\n# Render eyegaze classification plots')
+        mk_eyegaze_classification_figures()
--- a/img/.gitignore
+++ b/img/.gitignore
@ -3,6 +3,8 @@ confusion_MN_RA.*
 confusion_RA_AL.*
 remodnav_lab.*
 remodnav_mri.*
+rawtrace_lab.*
+rawtrace_mri.*
 remodnav_lab.pdf
 remodnav_mri.pdf
 confusion_MN_RA.pdf
--- a/img/Makefile
+++ b/img/Makefile
@ -1,21 +1,16 @@
 all: pics

-# Optionally some PICS could be ignored. By default XXX ones.
-# PICS_IGNORE must contain a rule for grep
-PICS_IGNORE ?= " "
+# use `chronic` to make output look neater, if available
+CHRONIC=$(shell which chronic || echo '' )

 # For every .svg we must have a pdf
-PICS=$(shell find . -iname \*svg \
-	| sed -e 's/svg/pdf/g' -e 's/\([^\]\)\([ \t:]\)/\1\\\\\2/g' \
-	| grep -v -e $(PICS_IGNORE) )
-
-pics: $(PICS)
-	echo $(PICS)
+pics: $(shell find . -iname \*.svg | sed -e 's/svg/pdf/g' )

 clean:
 	for p in *.svg; do rm -f $${p%*.svg}.eps $${p%*.svg}.pdf; done
 	-rm -rf *_300dpi.png

+# git-ignore each auto-rendered figure
 .PHONY: ignore-%
 ignore-%:
 	@grep -q "^$*$$" .gitignore || { \
@ -24,16 +19,9 @@ ignore-%:
 #
 # Inkscape rendered figures
 #
+# try modern-age API first, fall-back on old one, if needed
 %.pdf: %.svg ignore-%.pdf
 	@echo "Rendering $@"
-	@inkscape -z -f "$<" -A "$@" || inkscape --export-filename="$@" "$<"
-
-%.eps: %.svg ignore-%.eps
-	@echo "Rendering $@"
-	@inkscape -z -f "$<" -E "$@" || inkscape --export-filename="$@" "$<"
-
-%_300dpi.png: %.svg ignore-%_300dpi.png
-	@echo "Rendering $@"
-	@inkscape -z -f "$<" -e "$@" -d 300 || inkscape -d 300 --export-filename="$@" "$<"
+	@$(CHRONIC) inkscape --export-filename="$@" "$<" || $(CHRONIC) inkscape -z -f "$<" -A "$@"

 .PHONY: all pics