Merge pull request #54 from computational-psychology/manuscript

Update JOSS manuscript
computational-psychology · Mar 24, 2023 · bad3d76 · bad3d76
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diff --git a/manuscript/.github/workflows/draft-pdf.yml → .github/workflows/draft-pdf.yml b/manuscript/.github/workflows/draft-pdf.yml → .github/workflows/draft-pdf.yml
@@ -1,5 +1,8 @@
+name: Draft JOSS PDF
 
-on: [push]
+on:
+  push:
+    branches: [main, manuscript]
 
 jobs:
   paper:
@@ -13,13 +16,13 @@ jobs:
         with:
           journal: joss
           # This should be the path to the paper within your repo.
-          paper-path: paper.md
+          paper-path: manuscript/paper.md
       - name: Upload
         uses: actions/upload-artifact@v1
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled
           # PDF. Note, this should be the same directory as the input
           # paper.md
-          path: paper.pdf
+          path: manuscript/paper.pdf
 
diff --git a/.gitignore b/.gitignore
@@ -61,6 +61,8 @@ target/
 .vscode/
 
 *.png
+!manuscript/overview.png
+!manuscript/stimspace.png
 .pytest_cache/
 
 **/.ipynb_checkpoints/

diff --git a/manuscript/bibliography.bib b/manuscript/bibliography.bib
@@ -1,144 +1,220 @@
+@inproceedings{aguilar.maertens.ea2022,
+  title     = {Characterizing Perceptual Brightness Scales for {{White}}'s Effect Using Conjoint Measurement},
+  booktitle = {Journal of {{Vision}}},
+  author    = {Aguilar, Guillermo and Maertens, Marianne and Vincent, Joris},
+  year      = {2022},
+  month     = dec,
+  volume    = {22},
+  pages     = {3519},
+  address   = {{St. Pete Beach, FL}},
+  doi       = {10.1167/jov.22.14.3519},
+  urldate   = {2023-03-24},
+  langid    = {english}
+}
+
 @article{brainard1997,
-  title={The psychophysics toolbox},
-  author={Brainard, D. H.},
-  journal={Spatial vision},
-  volume={10},
-  number={4},
-  pages={433--436},
-  year={1997},
-  publisher={Netherlands Publisher: VSP},
-  doi={10.1163/156856897X00357},
+  title     = {The Psychophysics Toolbox},
+  author    = {Brainard, D. H.},
+  year      = {1997},
+  journal   = {Spatial vision},
+  volume    = {10},
+  number    = {4},
+  pages     = {433--436},
+  publisher = {{Netherlands Publisher: VSP}},
+  doi       = {10.1163/156856897X00357}
 }
 
 @inproceedings{carney1999,
-  title={Development of an image/threshold database for designing and testing human vision models},
-  author={Carney, T. and Klein, S. A. and Tyler, C. W. and Silverstein, A. D. and Beutter, B. and Levi, D. and Watson, A. B. and Reeves, A. J. and Norcia, A. M. and Chen, C.-C. and others},
-  booktitle={Human vision and electronic imaging IV},
-  volume={3644},
-  pages={542--551},
-  year={1999},
-  organization={SPIE},
-  doi={10.1117/12.348473},
+  title        = {Development of an Image/Threshold Database for Designing and Testing Human Vision Models},
+  booktitle    = {Human Vision and Electronic Imaging {{IV}}},
+  author       = {Carney, T. and Klein, S. A. and Tyler, C. W. and Silverstein, A. D. and Beutter, B. and Levi, D. and Watson, A. B. and Reeves, A. J. and Norcia, A. M. and Chen, C.-C. and others},
+  year         = {1999},
+  volume       = {3644},
+  pages        = {542--551},
+  doi          = {10.1117/12.348473},
+  organization = {{SPIE}}
 }
 
 @inproceedings{carney2000,
-  title={Modelfest: {Year} one results and plans for future years},
-  author={Carney, T. and Tyler, C. W. and Watson, A. B. and Makous, W. and Beutter, B. and Chen, C.-C. and Norcia, A. M. and Klein, S. A.},
-  booktitle={Human vision and electronic imaging V},
-  volume={3959},
-  pages={140--151},
-  year={2000},
-  organization={SPIE},
-  doi={10.1117/12.387150},
+  title        = {Modelfest: {{Year}} One Results and Plans for Future Years},
+  booktitle    = {Human Vision and Electronic Imaging {{V}}},
+  author       = {Carney, T. and Tyler, C. W. and Watson, A. B. and Makous, W. and Beutter, B. and Chen, C.-C. and Norcia, A. M. and Klein, S. A.},
+  year         = {2000},
+  volume       = {3959},
+  pages        = {140--151},
+  doi          = {10.1117/12.387150},
+  organization = {{SPIE}}
 }
 
 @inproceedings{deng2009,
-  title={Imagenet: A large-scale hierarchical image database},
-  author={Deng, J. and Dong, W. and Socher, R. and Li, L.-J. and Li, K. and Fei-Fei, L.},
-  booktitle={IEEE conference on computer vision and pattern recognition},
-  pages={248--255},
-  year={2009},
-  organization={IEEE},
-  doi={10.1109/CVPR.2009.5206848},
-}
-
-@article{peirce2019,
-  title={PsychoPy2: {E}xperiments in behavior made easy},
-  author={Peirce, J. and Gray, J. R. and Simpson, S. and MacAskill, M. and Hoechenberger, R. and Sogo, H. and Kastman, E. and Lindelov, J. K.},
-  journal={Behavior research methods},
-  volume={51},
-  number={1},
-  pages={195--203},
-  year={2019},
-  publisher={Springer},
-  doi={10.3758/s13428-018-01193-y},
+  title        = {Imagenet: {{A}} Large-Scale Hierarchical Image Database},
+  booktitle    = {{{IEEE}} Conference on Computer Vision and Pattern Recognition},
+  author       = {Deng, J. and Dong, W. and Socher, R. and Li, L.-J. and Li, K. and {Fei-Fei}, L.},
+  year         = {2009},
+  pages        = {248--255},
+  doi          = {10.1109/CVPR.2009.5206848},
+  organization = {{IEEE}}
 }
 
 @article{makowski2021,
-  title={A Parametric Framework to Generate Visual Illusions Using Python},
-  author={Makowski, D. and Lau, Z. J. and Pham, T. and Paul B., W. and Annabel C., S.},
-  journal={Perception},
-  volume={50},
-  number={11},
-  pages={950--965},
-  year={2021},
-  publisher={Sage Publications Sage UK: London, England},
-  doi={10.1177/03010066211057347},
+  title     = {A Parametric Framework to Generate Visual Illusions Using Python},
+  author    = {Makowski, D. and Lau, Z. J. and Pham, T. and Paul B., W. and Annabel C., S.},
+  year      = {2021},
+  journal   = {Perception},
+  volume    = {50},
+  number    = {11},
+  pages     = {950--965},
+  publisher = {{Sage Publications Sage UK: London, England}},
+  doi       = {10.1177/03010066211057347}
 }
 
 @inproceedings{martin2001,
-  author = {Martin, D. and Fowlkes, C. and Tal, D. and Malik, J.},
-  title = {A Database of Human Segmented Natural Images and its Application to Evaluating Segmentation Algorithms and Measuring Ecological Statistics},
-  booktitle = {8th IEEE Internatinonal Conference on Computer Vision},
-  year = {2001},
-  month = {July},
-  volume = {2},
-  pages = {416--423},
-  doi={10.1109/ICCV.2001.937655},
+  title     = {A Database of Human Segmented Natural Images and Its Application to Evaluating Segmentation Algorithms and Measuring Ecological Statistics},
+  booktitle = {8th {{IEEE}} Internatinonal Conference on Computer Vision},
+  author    = {Martin, D. and Fowlkes, C. and Tal, D. and Malik, J.},
+  year      = {2001},
+  month     = jul,
+  volume    = {2},
+  pages     = {416--423},
+  doi       = {10.1109/ICCV.2001.937655}
+}
+
+@article{murray2020,
+  title   = {A Model of Lightness Perception Guided by Probabilistic Assumptions about Lighting and Reflectance},
+  author  = {Murray, R. F.},
+  year    = {2020},
+  month   = jul,
+  journal = {Journal of Vision},
+  volume  = {20},
+  number  = {7},
+  pages   = {28},
+  issn    = {1534-7362},
+  doi     = {10/gh57gf},
+  urldate = {2021-03-01},
+  langid  = {english}
 }
 
 @article{murray2021,
-  title={Lightness perception in complex scenes},
-  author={Murray, R. F.},
-  journal={Annual Review of Vision Science},
-  volume={7},
-  year={2021},
-  publisher={Annual Reviews},
-  doi={10.1146/annurev-vision-093019-115159}
+  title     = {Lightness Perception in Complex Scenes},
+  author    = {Murray, R. F.},
+  year      = {2021},
+  journal   = {Annual Review of Vision Science},
+  volume    = {7},
+  publisher = {{Annual Reviews}},
+  doi       = {10.1146/annurev-vision-093019-115159}
+}
+
+@article{peirce2019,
+  title     = {{{PsychoPy2}}: {{Experiments}} in Behavior Made Easy},
+  author    = {Peirce, J. and Gray, J. R. and Simpson, S. and MacAskill, M. and Hoechenberger, R. and Sogo, H. and Kastman, E. and Lindelov, J. K.},
+  year      = {2019},
+  journal   = {Behavior research methods},
+  volume    = {51},
+  number    = {1},
+  pages     = {195--203},
+  publisher = {{Springer}},
+  doi       = {10.3758/s13428-018-01193-y}
 }
 
 @article{schmittwilken2022a,
-	type={Talk},
-	address = {Online},
-	title = {{BRENCH}: {An} open-source framework for b(r)enchmarking brightness models},
-	volume = {22},
-	copyright = {All rights reserved},
-	shorttitle = {Contributed {Session} {III}},
-	url = {https://jov.arvojournals.org/article.aspx?articleid=2778446},
-	doi = {10.1167/jov.22.3.36},
-	language = {en},
-	urldate = {2022-03-04},
-	booktitle = {Journal of {Vision}},
-	author = {Schmittwilken, L. and Matic, M. and Maertens, M. and Vincent, J.},
-	month = feb,
-	year = {2022},
-	pages = {36},
+  type       = {Talk},
+  title      = {{{BRENCH}}: {{An}} Open-Source Framework for b(r)Enchmarking Brightness Models},
+  shorttitle = {Contributed {{Session III}}},
+  author     = {Schmittwilken, L. and Matic, M. and Maertens, M. and Vincent, J.},
+  year       = {2022},
+  month      = feb,
+  journal    = {Journal of Vision},
+  volume     = {22},
+  pages      = {36},
+  address    = {{Online}},
+  doi        = {10.1167/jov.22.3.36},
+  urldate    = {2022-03-04},
+  copyright  = {All rights reserved},
+  langid     = {english}
 }
 
 @article{schmittwilken2022b,
-	title = {Fixational eye movements enable robust edge detection},
-	volume = {22},
-	doi = {10.1167/jov.22.8.5},
-	language = {en},
-	number = {8},
-	journal = {Journal of Vision},
-	author = {Schmittwilken, L. and Maertens, M.},
-	year = {2022},
-	pages = {1-12},
+  title   = {Fixational Eye Movements Enable Robust Edge Detection},
+  author  = {Schmittwilken, L. and Maertens, M.},
+  year    = {2022},
+  journal = {Journal of Vision},
+  volume  = {22},
+  number  = {8},
+  pages   = {1--12},
+  doi     = {10.1167/jov.22.8.5},
+  langid  = {english}
 }
 
 @article{schmittwilken2022c,
-	type={Poster},
-	address = {Online},
-	title = {Medium spatial frequencies mask edges most effectively},
-	volume = {22},
-	copyright = {All rights reserved},
-	doi = {10.1167/jov.22.14.4041},
-	booktitle = {Journal of {Vision}},
-	author = {Schmittwilken, L. and Maertens, M.},
-	month = dec,
-	year = {2022},
+  type      = {Poster},
+  title     = {Medium Spatial Frequencies Mask Edges Most Effectively},
+  author    = {Schmittwilken, L. and Maertens, M.},
+  year      = {2022},
+  month     = dec,
+  journal   = {Journal of Vision},
+  volume    = {22},
+  address   = {{Online}},
+  doi       = {10.1167/jov.22.14.4041},
+  copyright = {All rights reserved}
 }
 
-@article{wang2008,
-  title={Maximum differentiation {(MAD)} competition: {A} methodology for comparing computational models of perceptual quantities},
-  author={Wang, Z. and Simoncelli, E. P.},
-  journal={Journal of Vision},
-  volume={8},
-  number={12},
-  pages={8--8},
-  year={2008},
-  publisher={The Association for Research in Vision and Ophthalmology},
-  doi={10.1167/8.12.8}
+@misc{vincent.maertens.ea2021,
+  type    = {Talk},
+  title   = {Perceptual Brightness Scales in a {{White}}'s Effect Stimulus Are Not Captured by Multiscale Spatial Filtering Models of Brightness Perception},
+  author  = {Vincent, Joris and Maertens, Marianne and Aguilar, Guillermo},
+  year    = {2021},
+  month   = oct,
+  address = {{Online}},
+  langid  = {english}
+}
+
+@inproceedings{vincent.maertens.ea2022,
+  title     = {Perceptual {{Brightness Scales}} for {{White}}'s {{Effect Constrain Computational Models}} of {{Brightness Perception}}},
+  booktitle = {Journal of {{Vision}}},
+  author    = {Vincent, Joris and Maertens, Marianne and Aguilar, Guillermo},
+  year      = {2022},
+  month     = dec,
+  volume    = {22},
+  pages     = {4160},
+  address   = {{St. Pete Beach, FL}},
+  doi       = {10.1167/jov.22.14.4160},
+  urldate   = {2023-03-24},
+  langid    = {english}
+}
+
+@misc{vincent.maertens2021,
+  type    = {Talk},
+  title   = {The Missing Linking Functions in Computational Models of Brightness Perception},
+  author  = {Vincent, Joris and Maertens, Marianne},
+  year    = {2021},
+  month   = aug,
+  address = {{Online}},
+  langid  = {english}
 }
 
+@inproceedings{vincent.maertens2021a,
+  title     = {A History and Modular Future of Multiscale Spatial Filtering Models},
+  booktitle = {Journal of {{Vision}}},
+  author    = {Vincent, Joris and Maertens, Marianne},
+  year      = {2021},
+  month     = may,
+  volume    = {21},
+  pages     = {2824},
+  publisher = {{Journal of Vision}},
+  address   = {{Online}},
+  doi       = {10.1167/jov.21.9.2824},
+  urldate   = {2023-02-17},
+  langid    = {english}
+}
+
+@article{wang2008,
+  title     = {Maximum Differentiation ({{MAD}}) Competition: {{A}} Methodology for Comparing Computational Models of Perceptual Quantities},
+  author    = {Wang, Z. and Simoncelli, E. P.},
+  year      = {2008},
+  journal   = {Journal of Vision},
+  volume    = {8},
+  number    = {12},
+  pages     = {8--8},
+  publisher = {{The Association for Research in Vision and Ophthalmology}},
+  doi       = {10.1167/8.12.8}
+}
diff --git a/manuscript/overview.png b/manuscript/overview.png