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Reproducibility improvements #19

Merged
adswa merged 4 commits from reproducibility-improvements into master 2021-09-14 09:33:06 +00:00
Conversation 6 Commits 4 Files changed 23 +46914 -26
23 changed files with 46914 additions and 26 deletions
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2
Makefile
View file

@ -20,7 +20,7 @@ results_def.tex: code/mk_figuresnstats.py
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
@python -m pip install pandas==1.0.5 seaborn==0.10.1 scikit-learn==0.23.0 datalad
@datalad get -n remodnav
@$(CHRONIC) pip install -e remodnav
@rm -f $@

3
README.md
View file

@ -15,7 +15,8 @@ To recompute results and compile the paper, do the following:
```
- ``clone`` the repository with ``git clone https://github.com/psychoinformatics-de/paper-remodnav.git``
- Navigate into the repository and run ``make``
- Navigate into the repository and run ``make`` to compile the paper as it was published.
- To recompute results and figures, run ``make clean``, followed by ``make``.
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

21
code/mk_figuresnstats.py
View file

@ -30,6 +30,9 @@ from remodnav import (
)
from remodnav.tests import utils as ut
# configure matplotlib for deterministically named SVG identifiers.
from matplotlib import rcParams
rcParams['svg.hashsalt'] = 43
mih commented 2021-09-14 05:47:12 +00:00 (Migrated from github.com)
Copy link

Wouldn't it be 42? ;-)

Wouldn't it be 42? ;-)
adswa commented 2021-09-14 05:48:46 +00:00 (Migrated from github.com)
Copy link

I wanted to surprise people ;-)

I wanted to surprise people ;-)
#from remodnav.tests.test_labeled import load_data as load_anderson
def load_anderson(category, name):
@ -434,7 +437,8 @@ def mk_confusion_figures(fig, stat):
plt.savefig(
op.join('img', 'confusion_{}_{}.svg'.format(*pair)),
transparent=True,
bbox_inches="tight")
bbox_inches="tight",
metadata={'Date': None})
plt.close()
if cur_max_mclf > max_mclf:
max_mclf = cur_max_mclf
@ -530,7 +534,8 @@ def quality_stats():
plt.xscale('log')
plt.savefig(op.join('img', 'velhist.svg'),
transparent=True,
bbox_inches="tight")
bbox_inches="tight",
metadata={'Date': None})
def S2SRMS():
@ -808,7 +813,8 @@ def mk_raw_vel_trace_figures():
plt.savefig(
op.join('img', 'rawtrace_{}.svg'.format(ext)),
transparent=True,
bbox_inches="tight")
bbox_inches="tight",
metadata={'Date': None})
plt.close()
@ -869,7 +875,8 @@ def mk_eyegaze_classification_figures():
plt.savefig(
op.join('img', 'remodnav_{}.svg'.format(ext)),
transparent=True,
bbox_inches="tight")
bbox_inches="tight",
metadata={'Date': None})
plt.close()
# plot details
fig = plt.figure(
@ -983,7 +990,8 @@ def mk_mainseq_figures(s_mri, s_lab):
label,
ext)),
transparent=True,
bbox_inches="tight")
bbox_inches="tight",
metadata={'Date': None})
plt.close()
@ -1172,7 +1180,8 @@ def mk_event_duration_histograms(figures):
label,
ds_name)),
transparent=True,
bbox_inches="tight")
bbox_inches="tight",
metadata={'Date': None})
plt.close()

28
img/.gitignore vendored
View file

@ -1,29 +1,21 @@
confusion_MN_AL.*
confusion_MN_RA.*
confusion_RA_AL.*
remodnav_lab.*
remodnav_mri.*
rawtrace_lab.*
rawtrace_mri.*
confusion_MN_AL.pdf
confusion_MN_RA.pdf
confusion_RA_AL.pdf
remodnav_lab.pdf
remodnav_mri.pdf
rawtrace_lab.pdf
rawtrace_mri.pdf
remodnav_lab.pdf
remodnav_mri.pdf
confusion_MN_RA.pdf
remodnav_algorithm.pdf
mainseq_*
mainseq_*.pdf
mainseq_lab_300dpi.png
mainseq_mri_300dpi.png
mainseq_sub_lab_300dpi.png
mainseq_sub_mri_300dpi.png
confusion_RA_AL.pdf
confusion_MN_AL.pdf
hist_pursuit_lab.svg
hist_fixation_lab.svg
hist_PSO_lab.svg
hist_saccade_mri.svg
hist_saccade_lab.svg
hist_fixation_mri.svg
hist_PSO_mri.svg
hist_pursuit_mri.svg
hist_pursuit_lab.pdf
hist_fixation_lab.pdf
hist_PSO_lab.pdf
@ -36,8 +28,8 @@ mainseq_mri.pdf
mainseq_sub_lab.pdf
mainseq_lab.pdf
mainseq_sub_mri.pdf
remodnav_lab_detail.*
remodnav_mri_detail.*
remodnav_lab_detail.pdf
remodnav_mri_detail.pdf
vel_est_1.pdf
preproc.pdf
pseudocode.pdf

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img/hist_PSO_lab.svg Normal file
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@ -0,0 +1,846 @@
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