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Revision 2 #11

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AsimHDar merged 124 commits from revision_2 into master 2025-08-19 08:44:09 +00:00
Conversation 5 Commits 124 Files changed 18 +24509 -709

124 commits

Author SHA1 Message Date
Adina Wagner
73b8ac1a94 Merge branch 'revision_2' of github.com:ElectronicTeaCup/paper-remodnav into revision_2 2020-03-18 09:59:13 +01:00
Adina Wagner
5313d59c12 name parameter in caption 2020-03-18 09:59:06 +01:00
Michael Hanke
e257d8b3f7 Last detections 2020-03-18 09:58:34 +01:00
Adina Wagner
793d70cff4 Merge branch 'revision_2' of github.com:ElectronicTeaCup/paper-remodnav into revision_2 2020-03-18 09:24:03 +01:00
Adina Wagner
9856eaebc5 work towards a more extensive figure caption for algorithm overview 2020-03-18 09:23:56 +01:00
Michael Hanke
4a552bed95 Last bits 2020-03-18 09:23:40 +01:00
Michael Hanke
bec737e3dc Merge branch 'revision_2' of github.com:ElectronicTeaCup/paper-remodnav into revision_2 2020-03-18 08:55:42 +01:00
Michael Hanke
8eb8130a33 Tune methods 2020-03-18 08:55:32 +01:00
Adina Wagner
c5772f34eb Merge branch 'revision_2' of github.com:ElectronicTeaCup/paper-remodnav into revision_2 2020-03-18 08:29:25 +01:00
Adina Wagner
1c4767ea79 Label panels in flowchart 2020-03-18 08:29:14 +01:00
Michael Hanke
69a326ebf1 Tune abstract 2020-03-18 08:29:10 +01:00
Michael Hanke
83967caaf7 Merge branch 'revision_2' of github.com:ElectronicTeaCup/paper-remodnav into revision_2 2020-03-18 08:16:55 +01:00
Michael Hanke
10eb400d54 Update figure caption 2020-03-18 08:16:42 +01:00
Adina Wagner
a0f850dad0 increase opacity of arrow 2020-03-18 08:14:48 +01:00
Adina Wagner
2706567d4a Read paper once from start to end, adjusted all that needed it: 
- add a few Oxford commas
- remove instances of naturalistic and replace with dynamic & feature-rich,
where applicable
- mention stimulus size difference in velocity comparison
- improve description and references to Figures
 2020-03-13 11:28:33 +01:00
Adina Wagner
334a473b88 minor improvements to flowchart: 
increase fontsize a bit more
remove word 'window'
 2020-03-13 10:44:17 +01:00
Adina Wagner
5cf0219a71 plot mri data first 
this makes it easier to spot differences in the tail of the distributions
 2020-03-12 14:19:12 +01:00
Adina Wagner
1ae3910ade bf: orderly ref histogram 2020-03-12 14:10:36 +01:00
Adina Wagner
68a7be6cdd velocity versus dispersion-based: cite a few algorithms and an evaluation 2020-03-12 13:55:25 +01:00
Adina Wagner
be2116af26 plot velocity histogram with relative frequencies (within sample) 2020-03-12 13:53:26 +01:00
Adina Wagner
08053476d0 plot Butterworth-filtered time series for flowchart 2020-03-12 13:52:33 +01:00
Adina Wagner
4cb1643a3b Minor flowchart tune-ups: 
- large font size in figures
- color changes: consistently yellow display of adapting
thresholds, consistently red global thresholds, blue errors
 2020-03-12 13:51:48 +01:00
Adina Wagner
fb19050a6b add velocity plots to text, start to talk about differences 2020-03-10 14:12:07 +01:00
Adina Wagner
97a12b9838 add pdf histogram to .gitignore 2020-03-10 14:11:28 +01:00
Adina Wagner
eb78291a42 add code to plot velocity histograms 2020-03-10 14:10:55 +01:00
Adina Wagner
bf3caf60e0 add velocity histogram 
Because the computation of this figure takes about 20 min on
my computer, I'm adding it to Git. The function to calculate
it is quality_stats()
 2020-03-10 11:48:54 +01:00
Adina Wagner
747abde7fe non-movement -> non-eyemovement 2020-03-09 18:31:29 +01:00
Adina Wagner
d1062745cc remove trial structure from manuscript 2020-03-09 18:30:46 +01:00
Adina Wagner
8a3d815329 Title: change to dynamic stimulation 
sacrifices the V for the acronym, but there are no static videos
 2020-03-09 18:30:01 +01:00
Adina Wagner
dfb4ca5e0a reduce font size, highlight preproc detail 2020-03-09 18:29:13 +01:00
Adina Wagner
33703ab5e2 inspired by -> modeled after 2020-03-09 14:38:43 +01:00
Adina Wagner
edbaea0d7e TMP: commit old, minor improvements on prev flowchart 2020-03-09 14:35:28 +01:00
Adina Wagner
16e107eeaa use new flowchart for alg overview, change refs in text 
forgotten bracket
 2020-03-09 14:35:28 +01:00
Adina Wagner
2b4759aa45 start algorithm flowchart from scratch 
minor fixes to flowchart
 2020-03-09 14:35:26 +01:00
Adina Wagner
9e366daef9 add cautionary note about p-CR eye trackers and PSOs 2020-03-06 17:12:32 +01:00
Adina Wagner
f5ea70ce8c add frame of reference to fixation and pursuit definition 2020-03-06 17:11:13 +01:00
Adina Wagner
99b6d53f5d final purge of 'detection' 2020-03-06 17:10:41 +01:00
Adina Wagner
d45c5d7e89 compute avergage amount of signal loss in the two groups 2020-03-06 17:09:59 +01:00
Adina Wagner
cb33af2574 turn velocity calculation into function 2020-03-06 17:08:49 +01:00
Adina Wagner
55a31c956f remove duplicate reference 2020-03-06 12:08:15 +01:00
Adina Wagner
5f030173ea Raw gaze trace: Set ylimit to 2000deg/s 
(adjusted to highest velocity in mri sample)
 2020-03-06 12:06:49 +01:00
Adina Wagner
5ce1961a72 Change title to suggestion by reviewer 1 
as the term natural refers to head-fixed eye
tracking setups in the current eye tracking
literature
 2020-03-06 12:02:56 +01:00
Adina Wagner
69110c6cd7 second round of removing detection -- how did we miss so many? 2020-03-03 18:18:57 +01:00
Adina Wagner
10be9201a1 remove 'in contrast to NH' when talking about prolonged recordings 2020-03-03 15:31:32 +01:00
Adina Wagner
955fea3f88 Add quick-and-dirty draft of plotting function for raw samples 
fix y lims

replace detailed figures in gaze plots with plots of raw data

Adjust figure caption to new raw data plots

gitignore PDFs of raw data plots
 2020-03-03 15:31:29 +01:00
Adina Wagner
b84dc08b6e gitignore new algorithm flowchart pdf 2020-03-03 15:02:43 +01:00
Adina Wagner
a26b3fc1ce disable plotting of detail figure 
Reviewer 2 rightfully pointed out major flaws:
- plots only preprocessed data, not raw data
- unequal y axis scaling makes comparisons impossible
 2020-03-03 15:01:08 +01:00
Adina Wagner
1172b2d350 add draft of algorithm flowchart 2020-03-03 10:53:37 +01:00
Adina Wagner
111d05684b Less bold statement on detrimental effects of quality loss 2020-03-02 20:20:28 +01:00
Adina Wagner
ac22e2751d First round of reducing the term natural 2020-03-02 18:37:43 +01:00
Adina Wagner
020a38d179 On Jaccard indixes: 
- Add comment to publicly shared data in code
- Add interpretation of JI to main text
- Add data origin and computation details to table caption
- Change reproduce to inspired by
 2020-03-02 16:43:34 +01:00
Adina Wagner
18deab7794 Add Hessels et al. 2017 paper for example on adding artificial noise 2020-03-02 12:29:21 +01:00
Adina Wagner
be2dbad5fe Simplify reference management 
This helps when finding references and prevents accidental
duplicate references. Also, it makes the repository easier
to understand IMO. Specifically, it does the following:
- Put all references into a single file (references.bib)
- Remove existing duplicate references
- Unify formatting
- Remove files EyeGaze.bib and tools.bib (their refs are in references.bib
  now)
- Adjust Makefile (no EyeGaze.bib and tools.bib necessary to build main,
  instead references.bib)
- Adjust bibliography in main.tex
 2020-03-02 12:12:30 +01:00
Adina Wagner
3844652a8e Clarify single category PSO use in comparison 
also mention that high/low velocity PSO distinction is not used in
literature already now, as per request by reviewer 2
 2020-03-02 11:47:43 +01:00
Adina Wagner
0137c43005 rephrase: long-distance saccades -> large amplitude saccades 2020-03-02 11:20:24 +01:00
Adina Wagner
3c979e81ce Adjust citation: Stampe filter for preprocessing 
While NH use the Stampe filter, its not part of the algorithm
and only reported on in Friedman et al., 2018
 2020-03-02 11:17:57 +01:00
Asim H. Dar
f85a045529 small spacing corrections with /remodnav 2020-03-02 10:58:29 +01:00
Asim H. Dar
e368a6e788 reworded repoduction of table from Anderson to extended 2020-03-02 10:58:29 +01:00
Asim H. Dar
de5940fff9 reworded eye tracking recalibration sentence 2020-03-02 10:58:29 +01:00
Asim H. Dar
8f24f0e946 changed figure label for chunking time series chunking option 2020-03-02 10:58:29 +01:00
Asim H. Dar
65db8df86b reworded definition of smooth pursuits for clarity 2020-03-02 10:58:29 +01:00
Adina Wagner
12e8b67d7a
 		typo 2020-01-16 09:54:20 +01:00
Adina Wagner
a210e512f1
 		typo 2020-01-16 09:53:01 +01:00
Adina Wagner
b6c33aabd5
 		typo 2020-01-16 09:52:50 +01:00
Michael Hanke
5492ce3217 Go with a single accuracy quantification 2020-01-16 09:45:17 +01:00
Michael Hanke
f540145f69 Tune conclusions 2020-01-16 09:44:42 +01:00
Michael Hanke
8228b3490f Minor results fixups; add correct spatial accuracy estimates from paper 2020-01-16 09:23:20 +01:00
Michael Hanke
4c252a8c9e Methods section tuning, mostly figure captions 2020-01-16 08:54:43 +01:00
Michael Hanke
789b8a1036 Minor tuning of introduction 2020-01-16 08:13:53 +01:00
Michael Hanke
ea818fd6af Put generated results back into Git 
Enables to build the manuscript without the data analysis and diffs
between manuscript versions
 2020-01-16 07:30:34 +01:00
Adina Wagner
d1fefeaa64 remove "removed" and clarify dilate_nan 2020-01-15 18:24:02 +01:00
Adina Wagner
2ab573d241 tweak wrt open source in abstract 2020-01-15 14:36:19 +01:00
Adina Wagner
598c3a1386 move non-computable files from annex into git 2020-01-15 14:13:05 +01:00
Adina Wagner
bf154f4c41 content removed from git annex 2020-01-15 14:11:24 +01:00
Adina Wagner
6334df76c1 mention that the manuscript is a reproducible research object 2020-01-15 14:03:13 +01:00
Adina Wagner
bd3981ac05 remove leftover todos 2020-01-15 14:02:32 +01:00
Adina Wagner
f84fae0c09 few language tweaks 2020-01-15 14:02:16 +01:00
Adina Wagner
b450563758 update gitignore 2020-01-15 14:01:21 +01:00
Adina Wagner
1cbbb65296 mention independent validation by Dorr et al 2020-01-15 14:00:57 +01:00
Adina Wagner
435dcea3a4 content removed from git annex 2020-01-15 10:42:59 +01:00
Adina Wagner
d636656bd7 update .gitignore to detail svgs 2020-01-15 10:17:14 +01:00
Adina Wagner
72ce078964 get stuff out of annex 2019-12-19 10:32:05 +01:00
Adina Wagner
01bdefb59f content removed from git annex 2019-12-19 10:23:38 +01:00
Adina Wagner
185b440708 content removed from git annex 2019-12-19 10:23:32 +01:00
Adina Wagner
f0b45b627e minor tweaks, todo about quality measures for lab subjects 2019-08-14 16:40:50 +02:00
Adina Wagner
a6a0662911 add subsegment of remodnav output 2019-08-14 16:03:55 +02:00
Adina Wagner
c20f10f00b add subsegments of velocity-x-y figures to .gitignore 2019-08-14 16:03:22 +02:00
Adina Wagner
9d3fef6c50 clarify nulling around signal loss 2019-08-14 16:01:59 +02:00
Adina Wagner
9678b57394 add TODO about table 2019-08-14 15:16:14 +02:00
Adina Wagner
432f468242 restructure intro about definitions 2019-08-14 14:29:32 +02:00
Adina Wagner
1eb211a9df split overview figure into 3 illustrations plus pseudocode 2019-08-14 14:28:52 +02:00
Adina Wagner
3f18223568 add new individual overview img to gitignore 2019-08-14 14:28:09 +02:00
Adina Wagner
115fe07fdc add individual within ms window detection 2019-08-14 14:27:14 +02:00
Adina Wagner
abc5e1b282 add individual major saccade detection 2019-08-14 14:26:55 +02:00
Adina Wagner
daaad460de add individual pseudocode 2019-08-14 14:26:10 +02:00
Adina Wagner
675b5eb57a add individual preprocessing illustration 2019-08-14 14:25:28 +02:00
Adina Wagner
22989675fa add note about robustness analysis 2019-08-13 11:31:41 +02:00
Adina Wagner
da95a41af6 add short interpretation of Kappa results 2019-08-13 10:32:52 +02:00
Adina Wagner
f6c55d7249 add dense format as limitation 2019-08-13 10:14:04 +02:00
Adina Wagner
1f7e2ad965 add note on HPSO/LPSO distinction 2019-08-13 09:41:29 +02:00
Adina Wagner
cce23f15b6 stray space 2019-08-13 09:41:08 +02:00
Adina Wagner
6f20f3ec5e add reference about naturalistic experiments 2019-08-13 09:40:49 +02:00
Adina Wagner
b0ac4922bb add numbers on lower-quality 2019-08-13 08:00:54 +02:00
Adina Wagner
9001b5c6dd reduce usage of 'natural' 2019-08-12 15:57:47 +02:00
Adina Wagner
3d073ff527 detection -> classification 2019-08-12 15:57:22 +02:00
Adina Wagner
3eca235753 add Hessels 2018 paper, and include draft based on their suggestions 
They suggest adding computational, functional, and oculomotor definitions of eye movements, and specification of frames of reference
 2019-08-12 15:55:37 +02:00
Adina Wagner
9e5a0a3eaa embed details-figures in manuscript 2019-07-10 23:28:19 +02:00
Adina Wagner
a7f280be14 WIP: plot detail (total 0.5 sec) of remodnav output 
we should pick a segment where both time series have interesting events, also e.g. missing data.
 2019-07-10 23:25:00 +02:00
Michael Hanke
e24626ef3e More tweaks 2019-06-26 08:43:53 +02:00
Michael Hanke
ecc5c11882 Slightly more careful statement 2019-06-26 07:37:23 +02:00
Michael Hanke
ade72cef88 Add missing reference 2019-06-25 06:56:12 +02:00
Adina Wagner
1eb14a4578 REV1: include the frame of reference following reviewer advice in the intros summary of REMoDNaV. 
TODO: We might want to cite the paper as well
 2019-06-24 12:24:36 +02:00
Adina Wagner
c63e8c195f REV2: exchange 'measure' with 'method' 2019-06-24 11:36:33 +02:00
Adina Wagner
bc82ce9f9e REV2: exchange 'distinct imagery' with adjectives Asim proposed 2019-06-24 11:34:45 +02:00
Adina Wagner
1821e64619 REV1: very light editing to address notion about lack of definition in 'natural' stimuli and environment 2019-06-18 15:13:37 +02:00
Adina Wagner
18b7293cbf REV2: add small notion about REMoDNaV being FOSS to underline its 'new-ity' in intro. 
Not sure about phrasing and placement, but we can change/prettify that later
 2019-06-18 14:36:41 +02:00
Adina Wagner
cdb2adf23c REV2: exchange 'novel' with 'new' 2019-06-18 14:28:29 +02:00
Adina Wagner
f2d91758e7 REV1: remove remark about use for mobile or outdoor acquisition from conclusion 2019-06-18 14:24:14 +02:00
Adina Wagner
eb8b01fd65 format table, draft some initial text to go with it, cite Cohen for the measure 2019-06-18 14:18:51 +02:00
Adina Wagner
2c841afedc WIP: include Cohens Kappa table in manuscript. 
Currently the formatting is not good enough, but its a start.
 2019-06-18 11:22:32 +02:00
Adina Wagner
625d6caf53 include kappa() output in command line call to script 2019-06-18 11:21:41 +02:00
Adina Wagner
4ef75fcef4 print easier command names as kappa output 2019-06-18 11:21:15 +02:00
Adina Wagner
2b594fda34 Add a function to compute Cohens Kappa based on reviewer 2's request. 
The function computes Cohens Kappa as a measure of sample-wise similarity for each event type (fixation, saccade, PSO) for every stimulus type (img, dots, videos) between the coders and the algorithm and each coder
 2019-06-18 10:29:19 +02:00
Adina Wagner
1fdd49b8c3 make Anderson-to-REMoDNaV remapping global. 
Previously, the remapper was only necessary in the confusion computation, but as we need it for Cohens Kappa as well, I'm exposing it
 2019-06-18 10:24:59 +02:00