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2 changes: 0 additions & 2 deletions .travis.yml
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Expand Up @@ -29,8 +29,6 @@ before_install:
- ./miniconda.sh -b -p /home/travis/miniconda
- export PATH=/home/travis/miniconda/bin:$PATH
- conda update --yes --quiet conda
- "export DISPLAY=:99.0"
- "sh -e /etc/init.d/xvfb start"
- PACKAGES="python=${PYTHON_VERSION}"
- PACKAGES="${PACKAGES} numpy"; if [ ${NUMPY_VERSION} ]; then PACKAGES="${PACKAGES}=${NUMPY_VERSION}"; fi
- PACKAGES="${PACKAGES} scipy"; if [ ${SCIPY_VERSION} ]; then PACKAGES="${PACKAGES}=${SCIPY_VERSION}"; fi
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225 changes: 108 additions & 117 deletions BIBLIOGRAPHY.bib
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@@ -1,143 +1,134 @@
@phdthesis{Asano2015,
author = {Asano, Yuta},
school = {R.I.T.},
title = {{Individual Colorimetric Observers for Personalized
Color Imaging}},
year = 2015,
author = {Asano, Yuta},
file = {:Users/kelsolaar/Google Drive/Documents/Mendeley Desktop/Asano - 2015 - Individual Colorimetric Observers for Personalized Color Imaging.pdf:pdf},
school = {R.I.T.},
title = {{Individual Colorimetric Observers for Personalized Color Imaging}},
year = {2015}
}
@article{Breneman1987b,
abstract = {While each of his or her two eyes was independently adapted to a different illuminant in viewing a complex visual field, each of a number of observers matched a series of test colors seen by one eye with a juxtaposed variable stimulus seen by the other eye. The 2 degrees test and matching stimuli were located centrally in the complex adapting field, which subtended an angle of 31 degrees X 24 degrees. In making the matches, the observer viewed the test and matching stimuli for a series of brief intervals (approximately 1 sec) while viewing the complex adapting field with normal eye movements. Nine experiments were performed with different pairs of illuminants and different illuminances ranging from that of an average living room to that of a scene illuminated with hazy sunlight. In three other experiments each of the observer's two eyes was adapted to a different illuminance of D55. The amount of adaptation was more nearly complete at high levels of illuminance than at low levels, and the proportional amount of adaptation was less for the "blue" receptors. When adaptation coefficients were determined from the actual adaptation differences (e.g., from corresponding tristimulus values for matching neutrals) rather than from the adapting illuminants, a linear von Kries transformation based on experimentally determined visual primaries gave corresponding chromaticities that were in good agreement with the results obtained in each of the chromatic-adaptation experiments, except at the lowest illuminances. The results of the experiments in which each eye was adapted to different levels of the same illuminant indicated again that adaptation to the different levels was incomplete, the proportional amount of adaptation being less at low illuminances and for the "blue" receptors. This caused a change in chromatic adaptation with the level of illuminance even when the chromaticities of the adapting lights were equal. The results of these experiments also indicated that higher purities are needed in order to produce the same absolute color appearances at low levels of illuminance.},
author = {Breneman, Edwin J.},
doi = {10.1364/JOSAA.4.001115},
file = {:Users/kelsolaar/Google Drive/Documents/Mendeley Desktop/Breneman - 1987 - Corresponding chromaticities for different states of adaptation to complex visual fields.pdf:pdf;:Users/kelsolaar/Google Drive/Documents/Mendeley Desktop/Breneman - 1987 - Corresponding chromaticities for different states of adaptation to complex visual fields(2).pdf:pdf},
issn = {1084-7529},
journal = {Journal of the Optical Society of America A},
month = {jun},
number = {6},
pages = {1115},
pmid = {3598755},
title = {{Corresponding chromaticities for different states of adaptation to complex visual fields}},
url = {https://www.osapublishing.org/abstract.cfm?URI=josaa-4-6-1115 http://www.opticsinfobase.org/josaa/fulltext.cfm?uri=josaa-4-6-1115&id=2783},
volume = {4},
year = {1987}
}
@misc{Haanpalo,
author = {Haanpalo, Jouni and {University of Kuopio}},
doi = {10.5281/zenodo.3269916},
title = {{Munsell Colors Glossy (Spectrofotometer Measured)}},
url = {http://www.uef.fi/web/spectral/munsell-colors-glossy-spectrofotometer-measured},
author = {Haanpalo, Jouni and {University of Kuopio}},
doi = {10.5281/zenodo.3269916},
title = {{Munsell Colors Glossy (Spectrofotometer Measured)}},
url = {http://www.uef.fi/web/spectral/munsell-colors-glossy-spectrofotometer-measured}
}
@misc{Haanpaloa,
author = {Haanpalo, Jouni and {University of Kuopio}},
doi = {10.5281/zenodo.3269922},
title = {{Paper Spectra}},
url = {http://www.uef.fi/web/spectral/paper-spectra},
}
@misc{Hauta-Kasari,
author = {Hauta-Kasari, Markku and {University of Kuopio}},
doi = {10.5281/zenodo.3269912},
title = {{Munsell Colors Matt (Spectrofotometer Measured)}},
url = {http://www.uef.fi/web/spectral/munsell-colors-matt-spectrofotometer-measured},
author = {Haanpalo, Jouni and {University of Kuopio}},
doi = {10.5281/zenodo.3269922},
title = {{Paper Spectra}},
url = {http://www.uef.fi/web/spectral/paper-spectra}
}
@misc{Hauta-Kasaria,
author = {Hauta-Kasari, Markku and {University of Kuopio}},
doi = {10.5281/zenodo.3269914},
title = {{Munsell Colors Matt (AOTF Measured)}},
url = {http://www.uef.fi/web/spectral/munsell-colors-matt-aotf-measured-},
author = {Hauta-Kasari, Markku and {University of Kuopio}},
doi = {10.5281/zenodo.3269914},
title = {{Munsell Colors Matt (AOTF Measured)}},
url = {http://www.uef.fi/web/spectral/munsell-colors-matt-aotf-measured-}
}
@misc{Hauta-Kasari,
author = {Hauta-Kasari, Markku and {University of Kuopio}},
doi = {10.5281/zenodo.3269912},
title = {{Munsell Colors Matt (Spectrofotometer Measured)}},
url = {http://www.uef.fi/web/spectral/munsell-colors-matt-spectrofotometer-measured}
}
@misc{Hiltunen,
author = {Hiltunen, Jouni and {University of Kuopio}},
doi = {10.5281/zenodo.3269924},
title = {{Lumber Spectra}},
url = {http://www.uef.fi/web/spectral/lumber-spectra},
author = {Hiltunen, Jouni and {University of Kuopio}},
doi = {10.5281/zenodo.3269924},
title = {{Lumber Spectra}},
url = {http://www.uef.fi/web/spectral/lumber-spectra}
}
@inproceedings{Jiang2013,
abstract = {Camera spectral sensitivity functions relate scene
radiance with captured RGB triplets. They are important for many
computer vision tasks that use color information, such as
multispectral imaging, color rendering, and color constancy. In
this paper, we aim to explore the space of spectral sensitivity
functions for digital color cameras. After collecting a database
of 28 cameras covering a variety of types, we find this space
convex and two-dimensional. Based on this statistical model, we
propose two methods to recover camera spectral sensitivities using
regular reflective color targets (e.g., color checker) from a
single image with and without knowing the illumination. We show
the proposed model is more accurate and robust for estimating
camera spectral sensitivities than other basis functions. We also
show two applications for the recovery of camera spectral
sensitivities - simulation of color rendering for cameras and
computational color constancy.},
author = {Jiang, Jun and Liu, Dengyu and Gu, Jinwei and
Susstrunk, Sabine},
booktitle = {2013 IEEE Workshop on Applications of Computer
Vision (WACV)},
doi = {10.1109/WACV.2013.6475015},
isbn = {978-1-4673-5054-9},
issn = 21583978,
month = jan,
pages = {168--179},
publisher = {IEEE},
title = {{What is the space of spectral sensitivity functions
for digital color cameras?}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6475015},
year = 2013,
abstract = {Camera spectral sensitivity functions relate scene radiance with captured RGB triplets. They are important for many computer vision tasks that use color information, such as multispectral imaging, color rendering, and color constancy. In this paper, we aim to explore the space of spectral sensitivity functions for digital color cameras. After collecting a database of 28 cameras covering a variety of types, we find this space convex and two-dimensional. Based on this statistical model, we propose two methods to recover camera spectral sensitivities using regular reflective color targets (e.g., color checker) from a single image with and without knowing the illumination. We show the proposed model is more accurate and robust for estimating camera spectral sensitivities than other basis functions. We also show two applications for the recovery of camera spectral sensitivities - simulation of color rendering for cameras and computational color constancy.},
author = {Jiang, Jun and Liu, Dengyu and Gu, Jinwei and Susstrunk, Sabine},
booktitle = {2013 IEEE Workshop on Applications of Computer Vision (WACV)},
doi = {10.1109/WACV.2013.6475015},
file = {:Users/kelsolaar/Google Drive/Documents/Mendeley Desktop/Jiang et al. - 2013 - What is the space of spectral sensitivity functions for digital color cameras.pdf:pdf},
isbn = {978-1-4673-5054-9},
issn = {21583978},
month = {jan},
pages = {168--179},
publisher = {IEEE},
title = {{What is the space of spectral sensitivity functions for digital color cameras?}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6475015},
year = {2013}
}
@misc{Labsphere2019,
author = {Labsphere},
doi = {10.5281/zenodo.3245875},
title = {{Labsphere SRS-99-020}},
year = 2019,
author = {Labsphere},
doi = {10.5281/zenodo.3245875},
title = {{Labsphere SRS-99-020}},
year = {2019}
}
@article{Luo1999,
abstract = {Predicting the binding mode of flexible polypeptides
to proteins is an important task that falls outside the domain of
applicability of most small molecule and protein−protein docking
tools. Here, we test the small molecule flexible ligand docking
program Glide on a set of 19 non-$\alpha$-helical peptides and
systematically improve pose prediction accuracy by enhancing Glide
sampling for flexible polypeptides. In addition, scoring of the
poses was improved by post-processing with physics-based implicit
solvent MM- GBSA calculations. Using the best RMSD among the top
10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 {\AA}
for the interface backbone atoms) increased from 21% with default
Glide SP settings to 58% with the enhanced peptide sampling and
scoring protocol in the case of redocking to the native protein
structure. This approaches the accuracy of the recently developed
Rosetta FlexPepDock method (63% success for these 19 peptides)
while being over 100 times faster. Cross-docking was performed for
a subset of cases where an unbound receptor structure was
available, and in that case, 40% of peptides were docked
successfully. We analyze the results and find that the optimized
polypeptide protocol is most accurate for extended peptides of
limited size and number of formal charges, defining a domain of
applicability for this approach.},
author = {Luo, M. Ronnier and Rhodes, Peter A.},
doi = {10.1002/(SICI)1520-6378(199908)24:4<295::AID-COL10>3.0.CO;2-K},
issn = {0361-2317},
journal = {Color Research \& Application},
month = aug,
number = 4,
pages = {295--296},
title = {{Corresponding-colour datasets}},
url = {http://doi.wiley.com/10.1002/%28SICI%291520-6378%28199908%2924%3A4%3C295%3A%3AAID-COL10%3E3.0.CO%3B2-K},
volume = 24,
year = 1999,
abstract = {Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-$\alpha$-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 {\AA} for the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40% of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.},
author = {Luo, M. Ronnier and Rhodes, Peter A.},
doi = {10.1002/(SICI)1520-6378(199908)24:4<295::AID-COL10>3.0.CO;2-K},
file = {:Users/kelsolaar/Google Drive/Documents/Mendeley Desktop/Luo, Rhodes - 1999 - Corresponding-colour datasets.pdf:pdf},
issn = {0361-2317},
journal = {Color Research & Application},
month = {aug},
number = {4},
pages = {295--296},
title = {{Corresponding-colour datasets}},
url = {http://doi.wiley.com/10.1002/%28SICI%291520-6378%28199908%2924%3A4%3C295%3A%3AAID-COL10%3E3.0.CO%3B2-K},
volume = {24},
year = {1999}
}
@misc{Marszalec,
author = {Marszalec, Elzbieta and {University of Kuopio}},
doi = {10.5281/zenodo.3269926},
title = {{Agfa IT8.7/2 Set}},
url = {http://www.uef.fi/web/spectral/agfa-it8.7/2-set},
author = {Marszalec, Elzbieta and {University of Kuopio}},
doi = {10.5281/zenodo.3269926},
title = {{Agfa IT8.7/2 Set}},
url = {http://www.uef.fi/web/spectral/agfa-it8.7/2-set}
}
@article{McCann1976,
author = {McCann, John J. and McKee, Suzanne P. and Taylor, Thomas H},
doi = {10.1016/0042-6989(76)90020-1},
file = {:Users/kelsolaar/Google Drive/Documents/Mendeley Desktop/McCann, McKee, Taylor - 1976 - Quantitative studies in retinex theory a comparison between theoretical predictions and observer resp.pdf:pdf},
issn = {00426989},
journal = {Vision Research},
month = {jan},
number = {5},
pages = {445--IN3},
title = {{Quantitative studies in retinex theory a comparison between theoretical predictions and observer responses to the “color mondrian” experiments}},
url = {https://linkinghub.elsevier.com/retrieve/pii/0042698976900201},
volume = {16},
year = {1976}
}
@misc{OpenpyxlDevelopers2019,
author = {{Openpyxl Developers}},
title = {openpyxl},
url = {https://bitbucket.org/openpyxl/openpyxl/},
year = 2019,
author = {{Openpyxl Developers}},
title = {openpyxl},
url = {https://bitbucket.org/openpyxl/openpyxl/},
year = {2019}
}
@misc{Orava,
author = {Orava, Joni and {University of Kuopio}},
doi = {10.5281/zenodo.3269918},
title = {{Munsell Colors Glossy (All) (Spectrofotometer
Measured)}},
url = {http://www.uef.fi/web/spectral/munsell-colors-glossy-all-spectrofotometer-measured},
author = {Orava, Joni and {University of Kuopio}},
doi = {10.5281/zenodo.3269918},
title = {{Munsell Colors Glossy (All) (Spectrofotometer Measured)}},
url = {http://www.uef.fi/web/spectral/munsell-colors-glossy-all-spectrofotometer-measured}
}
@misc{Silvennoinen,
author = {Silvennoinen, Raimo and {University of Kuopio}},
doi = {10.5281/zenodo.3269920},
title = {{Forest Colors}},
url = {http://www.uef.fi/web/spectral/forest-colors},
author = {Silvennoinen, Raimo and {University of Kuopio}},
doi = {10.5281/zenodo.3269920},
title = {{Forest Colors}},
url = {http://www.uef.fi/web/spectral/forest-colors}
}
@misc{X-Rite2016,
author = {X-Rite},
title = {{New Color Specifications for ColorChecker SG and
Classic Charts}},
url = {https://xritephoto.com/ph_product_overview.aspx?ID=938\&Action=Support\&SupportID=5884},
urldate = {2019-06-14},
year = 2016,
author = {X-Rite},
title = {{New Color Specifications for ColorChecker SG and Classic Charts}},
url = {https://xritephoto.com/ph_product_overview.aspx?ID=938&Action=Support&SupportID=5884},
urldate = {2019-06-14},
year = {2016}
}
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