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Built color selection infrastructure and assigned stage-specific colors (WIP).

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Added 2 plots to methods (WIP).
This commit is contained in:
j-hartling 2026-02-17 16:46:02 +01:00
parent d78dcf4f4a
commit 49b2bdcfca
16 changed files with 631 additions and 173 deletions
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6
.gitignore vendored
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@ -1,2 +1,6 @@
data/* # Python:
./__pycache__/ ./__pycache__/
*.py[cod]
*$py.class
# Recording data:
data/*

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main.aux
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@ -222,7 +222,9 @@
\abx@aux@page{68}{7} \abx@aux@page{68}{7}
\abx@aux@page{69}{7} \abx@aux@page{69}{7}
\newlabel{eq:highpass}{{4}{7}{}{}{}} \newlabel{eq:highpass}{{4}{7}{}{}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2}Feature extraction by individual neurons}{7}{}\protected@file@percent } \@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces \relax }}{8}{}\protected@file@percent }
\newlabel{fig:pre}{{2}{8}{}{}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2}Feature extraction by individual neurons}{8}{}\protected@file@percent }
\newlabel{eq:conv}{{5}{8}{}{}{}} \newlabel{eq:conv}{{5}{8}{}{}{}}
\newlabel{eq:gabor}{{6}{8}{}{}{}} \newlabel{eq:gabor}{{6}{8}{}{}{}}
\abx@aux@cite{0}{ronacher1986routes} \abx@aux@cite{0}{ronacher1986routes}
@ -237,23 +239,25 @@
\abx@aux@page{70}{9} \abx@aux@page{70}{9}
\abx@aux@page{71}{9} \abx@aux@page{71}{9}
\abx@aux@page{72}{9} \abx@aux@page{72}{9}
\newlabel{eq:lowpass}{{10}{9}{}{}{}} \newlabel{eq:lowpass}{{10}{10}{}{}{}}
\@writefile{toc}{\contentsline {section}{\numberline {3}Two mechanisms driving the emergence of intensity-invariant song representation}{9}{}\protected@file@percent } \@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces \relax }}{10}{}\protected@file@percent }
\newlabel{fig:stages_feat}{{3}{10}{}{}{}}
\@writefile{toc}{\contentsline {section}{\numberline {3}Two mechanisms driving the emergence of intensity-invariant song representation}{10}{}\protected@file@percent }
\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Logarithmic scaling \& spike-frequency adaptation}{10}{}\protected@file@percent } \@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Logarithmic scaling \& spike-frequency adaptation}{10}{}\protected@file@percent }
\newlabel{eq:toy_env}{{11}{10}{}{}{}} \newlabel{eq:toy_env}{{11}{11}{}{}{}}
\newlabel{eq:toy_snr}{{12}{10}{}{}{}} \newlabel{eq:toy_snr}{{12}{11}{}{}{}}
\newlabel{eq:toy_log}{{13}{10}{}{}{}} \newlabel{eq:toy_log}{{13}{11}{}{}{}}
\newlabel{eq:toy_highpass}{{14}{11}{}{}{}} \newlabel{eq:toy_highpass}{{14}{11}{}{}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Threshold nonlinearity \& temporal averaging}{11}{}\protected@file@percent } \@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Threshold nonlinearity \& temporal averaging}{12}{}\protected@file@percent }
\newlabel{eq:pdf_split}{{15}{11}{}{}{}} \newlabel{eq:pdf_split}{{15}{12}{}{}{}}
\newlabel{eq:pdf}{{16}{11}{}{}{}} \newlabel{eq:pdf}{{16}{12}{}{}{}}
\newlabel{eq:feat_avg}{{17}{12}{}{}{}} \newlabel{eq:feat_avg}{{17}{12}{}{}{}}
\newlabel{eq:feat_prop}{{18}{12}{}{}{}} \newlabel{eq:feat_prop}{{18}{13}{}{}{}}
\abx@aux@cite{0}{stumpner1991auditory} \abx@aux@cite{0}{stumpner1991auditory}
\abx@aux@segm{0}{0}{stumpner1991auditory} \abx@aux@segm{0}{0}{stumpner1991auditory}
\@writefile{toc}{\contentsline {section}{\numberline {4}Discriminating species-specific song\\patterns in feature space}{13}{}\protected@file@percent } \@writefile{toc}{\contentsline {section}{\numberline {4}Discriminating species-specific song\\patterns in feature space}{14}{}\protected@file@percent }
\@writefile{toc}{\contentsline {section}{\numberline {5}Conclusions \& outlook}{13}{}\protected@file@percent } \@writefile{toc}{\contentsline {section}{\numberline {5}Conclusions \& outlook}{14}{}\protected@file@percent }
\abx@aux@page{73}{13} \abx@aux@page{73}{14}
\gdef\svg@ink@ver@settings{{\m@ne }{inkscape}{\m@ne }} \gdef\svg@ink@ver@settings{{\m@ne }{inkscape}{\m@ne }}
\abx@aux@read@bbl@mdfivesum{1380DC8C93D2855FDB132CC5A40AD52F} \abx@aux@read@bbl@mdfivesum{1380DC8C93D2855FDB132CC5A40AD52F}
\gdef \@abspage@last{13} \gdef \@abspage@last{14}

44
main.bbl-SAVE-ERROR
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@ -1951,19 +1951,19 @@
\range{pages}{10} \range{pages}{10}
\endentry \endentry
\entry{stumpner1994song}{article}{} \entry{stumpner1994song}{article}{}
\name{author}{2}{}{% \name{author}{2}{ul=2}{%
{{un=0,uniquepart=base,hash=a7bef35fb61ea64e0f04d6c87e5aa622}{% {{un=0,uniquepart=base,hash=a7bef35fb61ea64e0f04d6c87e5aa622}{%
family={Stumpner}, family={Stumpner},
familyi={S\bibinitperiod}, familyi={S\bibinitperiod},
given={Andreas}, given={Andreas},
giveni={A\bibinitperiod}, giveni={A\bibinitperiod},
givenun=0}}% givenun=0}}%
{{un=0,uniquepart=base,hash=ecb958a09c71420bd1e10f3fee8c24ac}{% {{un=1,uniquepart=given,hash=ecb958a09c71420bd1e10f3fee8c24ac}{%
family={Helversen}, family={Helversen},
familyi={H\bibinitperiod}, familyi={H\bibinitperiod},
given={Otto}, given={Otto},
giveni={O\bibinitperiod}, giveni={O\bibinitperiod},
givenun=0, givenun=1,
prefix={von}, prefix={von},
prefixi={v\bibinitperiod}, prefixi={v\bibinitperiod},
prefixun=0}}% prefixun=0}}%
@ -1987,6 +1987,44 @@
\field{pages}{1\bibrangedash 23} \field{pages}{1\bibrangedash 23}
\range{pages}{23} \range{pages}{23}
\endentry \endentry
\entry{stumpner1991auditory}{article}{}
\name{author}{2}{ul=2}{%
{{un=0,uniquepart=base,hash=a7bef35fb61ea64e0f04d6c87e5aa622}{%
family={Stumpner},
familyi={S\bibinitperiod},
given={Andreas},
giveni={A\bibinitperiod},
givenun=0}}%
{{un=0,uniquepart=base,hash=4ce9349f95ced7a4831a5efa0fe5b00f}{%
family={Ronacher},
familyi={R\bibinitperiod},
given={Bernhard},
giveni={B\bibinitperiod},
givenun=0}}%
}
\list{publisher}{1}{%
{The Company of Biologists Ltd}%
}
\strng{namehash}{c6b9dac84d9d74ba87037123f4e21034}
\strng{fullhash}{c6b9dac84d9d74ba87037123f4e21034}
\strng{bibnamehash}{c6b9dac84d9d74ba87037123f4e21034}
\strng{authorbibnamehash}{c6b9dac84d9d74ba87037123f4e21034}
\strng{authornamehash}{c6b9dac84d9d74ba87037123f4e21034}
\strng{authorfullhash}{c6b9dac84d9d74ba87037123f4e21034}
\field{sortinit}{S}
\field{sortinithash}{b164b07b29984b41daf1e85279fbc5ab}
\field{extradatescope}{labelyear}
\field{labeldatesource}{}
\field{labelnamesource}{author}
\field{labeltitlesource}{title}
\field{journaltitle}{Journal of Experimental Biology}
\field{number}{1}
\field{title}{Auditory interneurones in the metathoracic ganglion of the grasshopper Chorthippus biguttulus: I. Morphological and physiological characterization}
\field{volume}{158}
\field{year}{1991}
\field{pages}{391\bibrangedash 410}
\range{pages}{20}
\endentry
\entry{suga1960peripheral}{article}{} \entry{suga1960peripheral}{article}{}
\name{author}{1}{}{% \name{author}{1}{}{%
{{un=0,uniquepart=base,hash=cb8492490b7b1d1c021ccd740577eab6}{% {{un=0,uniquepart=base,hash=cb8492490b7b1d1c021ccd740577eab6}{%

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[0] Config.pm:307> INFO - This is Biber 2.19 [0] Config.pm:307> INFO - This is Biber 2.19
[0] Config.pm:310> INFO - Logfile is 'main.blg' [0] Config.pm:310> INFO - Logfile is 'main.blg'
[35] biber:340> INFO - === Do Feb 12, 2026, 15:55:36 [36] biber:340> INFO - === Di Feb 17, 2026, 16:10:35
[42] Biber.pm:419> INFO - Reading 'main.bcf' [43] Biber.pm:419> INFO - Reading 'main.bcf'
[69] Biber.pm:979> INFO - Found 55 citekeys in bib section 0 [71] Biber.pm:979> INFO - Found 55 citekeys in bib section 0
[74] Biber.pm:4419> INFO - Processing section 0 [76] Biber.pm:4419> INFO - Processing section 0
[78] Biber.pm:4610> INFO - Looking for bibtex file 'cite.bib' for section 0 [80] Biber.pm:4610> INFO - Looking for bibtex file 'cite.bib' for section 0
[80] bibtex.pm:1713> INFO - LaTeX decoding ... [82] bibtex.pm:1713> INFO - LaTeX decoding ...
[110] bibtex.pm:1519> INFO - Found BibTeX data source 'cite.bib' [111] bibtex.pm:1519> INFO - Found BibTeX data source 'cite.bib'
[282] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' [277] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
[282] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' [277] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
[282] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US' [277] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
[282] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US' [277] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
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[314] bbl.pm:763> INFO - Output to main.bbl [310] bbl.pm:763> INFO - Output to main.bbl
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 10, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 10, warning: 6 characters of junk seen at toplevel
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[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 38, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 38, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 49, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 49, warning: 6 characters of junk seen at toplevel
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[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 73, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 73, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 82, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 82, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 91, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 91, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 100, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 100, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 109, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 109, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 118, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 118, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 127, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 127, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 136, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 136, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 157, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 157, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 178, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 178, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 187, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 187, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 196, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 196, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 207, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 207, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 218, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 218, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 229, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 229, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 240, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 240, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 249, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 249, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 258, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 258, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 269, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 269, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 278, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 278, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 289, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 289, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 300, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 300, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 309, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 309, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 328, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 328, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 337, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 337, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 400, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 400, warning: 6 characters of junk seen at toplevel
[314] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 419, warning: 6 characters of junk seen at toplevel [310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 419, warning: 6 characters of junk seen at toplevel
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[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 491, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 491, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 526, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 526, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 535, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 535, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 556, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 556, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 565, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 565, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 576, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 576, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 587, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 587, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 619, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 619, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 648, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 648, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 658, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 658, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 667, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 667, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 688, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 688, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 709, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 709, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 720, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 720, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 729, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 729, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 749, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 749, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 766, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 766, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 775, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 775, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 800, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 800, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_kvhD/347c261ec4135a5723bef5c751f5078f_27267.utf8, line 817, warning: 6 characters of junk seen at toplevel [311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 817, warning: 6 characters of junk seen at toplevel
[315] Biber.pm:133> INFO - WARNINGS: 55 [311] Biber.pm:133> INFO - WARNINGS: 55

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main.fdb_latexmk
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@ -1,14 +1,14 @@
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main.tex
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@ -409,6 +409,14 @@ intensity-adapted envelope $\adapt(t)$ is then passed on from the local
interneurons to the ascending neurons, where it serves as the basis for the interneurons to the ascending neurons, where it serves as the basis for the
following feature extraction stage. following feature extraction stage.
\begin{figure}[!ht]
\centering
\includegraphics[width=\textwidth]{figures/pathway_stages_pre.pdf}
\caption{}
\label{fig:pre}
\end{figure}
\FloatBarrier
\subsection{Feature extraction by individual neurons} \subsection{Feature extraction by individual neurons}
The ascending neurons extract and encode a number of different features of the The ascending neurons extract and encode a number of different features of the
@ -508,6 +516,14 @@ the resulting high-dimensional feature space, different species-specific song
patterns are characterized by a distinct combination of feature values, which patterns are characterized by a distinct combination of feature values, which
can be read out by a simple linear classifier. can be read out by a simple linear classifier.
\begin{figure}[!ht]
\centering
\includegraphics[width=\textwidth]{figures/pathway_stages_feat.pdf}
\caption{}
\label{fig:stages_feat}
\end{figure}
\FloatBarrier
\section{Two mechanisms driving the emergence of intensity-invariant song representation} \section{Two mechanisms driving the emergence of intensity-invariant song representation}
\textbf{Definition of invariance (general, systemic):}\\ \textbf{Definition of invariance (general, systemic):}\\

227
python/fig_pathway_stages.py
View File

@ -1,34 +1,123 @@
import glob
import plotstyle_plt import plotstyle_plt
import glob
import numpy as np import numpy as np
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from itertools import product
from thunderhopper.modeltools import load_data from thunderhopper.modeltools import load_data
from IPython import embed from IPython import embed
def prepare_fig(nrows, ncols, width=8, height=None, rheight=2,
left=0.01, right=0.95, bottom=0.01, top=0.95,
wspace=0.4, hspace=0.4):
if height is None:
height = rheight * nrows
fig = plt.figure(figsize=(width, height))
grid = fig.add_gridspec(nrows=nrows, ncols=ncols, wspace=wspace, hspace=hspace,
left=left, right=right, top=top, bottom=bottom)
axes = np.zeros((nrows, ncols), dtype=object)
for i, j in product(range(nrows), range(ncols)):
axes[i, j] = fig.add_subplot(grid[i, j])
axes[i, j].set_facecolor('none')
return fig, axes
def xlimits(ax, time, minval=None, maxval=None, pad=0.05):
limits = [minval, maxval]
if minval is None:
limits[0] = time[0]
if maxval is None:
limits[1] = time[-1]
if pad is not None and minval is None:
limits[0] -= (limits[1] - limits[0]) * pad
if pad is not None and maxval is None:
limits[1] += (limits[1] - limits[0]) * pad
return ax.set_xlim(limits)
def ylimits(ax, signal, minval=None, maxval=None, pad=0.05):
limits = [minval, maxval]
if minval is None:
limits[0] = signal.min()
if maxval is None:
limits[1] = signal.max()
if pad is not None and minval is None:
limits[0] -= (limits[1] - limits[0]) * pad
if pad is not None and maxval is None:
limits[1] += (limits[1] - limits[0]) * pad
return ax.set_ylim(limits)
def super_xlabel(label, fig, high_ax, low_ax, **kwargs):
x = (low_ax.get_position().x0 + high_ax.get_position().x1) / 2
fig.supxlabel(label, x=x, **kwargs)
return None
def super_ylabel(label, fig, high_ax, low_ax, **kwargs):
y = (low_ax.get_position().y0 + high_ax.get_position().y1) / 2
fig.supylabel(label, y=y, **kwargs)
return None
def hide_axis(ax, side='bottom'):
ax.spines[side].set_visible(False)
params = {side: False, 'label' + side: False}
ax.tick_params(axis='x' if side in ['top', 'bottom'] else 'y',
which='both', **params)
return None
def plot_line(ax, time, signal, ymin=None, ymax=None, xmin=None, xmax=None,
xpad=None, ypad=0.05, **kwargs):
ax.plot(time, signal, **kwargs)
xlimits(ax, time, minval=xmin, maxval=xmax, pad=xpad)
ylimits(ax, signal, minval=ymin, maxval=ymax, pad=ypad)
return None
def plot_barcode(ax, time, binary, offset=0.1, xmin=None, xmax=None, **kwargs):
if xmin is None:
xmin = time[0]
if xmax is None:
xmax = time[-1]
lower, upper = 0, 1
for i in range(binary.shape[1]):
ax.fill_between(time, lower, upper, where=binary[:, i], **kwargs)
if i < binary.shape[1] - 1:
lower += offset + 1
upper += offset + 1
xlimits(ax, time, minval=xmin, maxval=xmax)
ax.set_ylim(0, upper)
ax.axis('off')
return None
def indicate_zoom(fig, high_ax, low_ax, zoom_abs, **kwargs):
y0 = low_ax.get_position().y0
y1 = high_ax.get_position().y1
transform = low_ax.transData + fig.transFigure.inverted()
x0 = transform.transform((zoom_abs[0], 0))[0]
x1 = transform.transform((zoom_abs[1], 0))[0]
rect = plt.Rectangle((x0, y0), x1 - x0, y1 - y0,
transform=fig.transFigure, **kwargs)
fig.add_artist(rect)
return None
# GENERAL SETTINGS: # GENERAL SETTINGS:
data_paths = glob.glob('../data/processed/*.npz') target = 'Omocestus_rufipes'
stages = ['filt', 'env', 'log', 'inv', data_paths = glob.glob(f'../data/processed/{target}*.npz')
'conv', 'bi', 'feat'] stages = ['filt', 'env', 'log', 'inv', 'conv', 'bi', 'feat']
channel = 0 save_name = '../figures/pathway_stages'
# PLOT SETTINGS: # PLOT SETTINGS:
fig_kwargs = dict( fig_kwargs = dict(
figsize = np.array([16, 9]) * 0.75, width=16 / 2.54 * 2,
layout = 'constrained', height=6 / 2.54 * 2,
sharex = 'col', rheight=2 / 2.54 * 2,
sharey = 'row'
) )
zoom_rel = np.array([0.4, 0.6]) grid_kwargs = dict(
colors = dict( wspace=0.15,
filt='k', hspace=0.3,
env='k', left=0.1,
log='k', right=0.95,
inv='k', bottom=0.1,
conv='k', top=0.95
bi='k',
feat='k'
) )
linewidths = dict( colors = {s: c.item() for s, c in dict(np.load('../data/stage_colors.npz')).items()}
lw_full = dict(
filt=0.25, filt=0.25,
env=0.5, env=0.5,
log=0.5, log=0.5,
@ -37,11 +126,24 @@ linewidths = dict(
bi=1, bi=1,
feat=1 feat=1
) )
lw_zoom = dict(
filt=0.25,
env=0.75,
log=0.75,
inv=0.75,
conv=0.5,
bi=1,
feat=0.75
)
zoom_rel = np.array([0.3, 0.4])
zoom_kwargs = dict(
color=(0.85, 0.85, 0.85),
zorder=0,
linewidth=0
)
# EXECUTION: # EXECUTION:
for data_path in data_paths: for data_path in data_paths:
if 'Gomphocerippus' in data_path:
continue
print(f'Processing {data_path}') print(f'Processing {data_path}')
# Load overall data: # Load overall data:
@ -55,79 +157,80 @@ for data_path in data_paths:
# PART I: PREPROCESSING STAGE # PART I: PREPROCESSING STAGE
fig, axes = plt.subplots(4, 2, **fig_kwargs) fig, axes = prepare_fig(4, 2, **fig_kwargs, **grid_kwargs)
fig.supylabel('amplitude', fontsize=plt.rcParams['axes.labelsize']) super_xlabel('time [s]', fig, axes[0, 0], axes[0, -1])
fig.supxlabel('time [s]', fontsize=plt.rcParams['axes.labelsize']) super_ylabel('amplitude', fig, axes[0, 0], axes[-1, 0])
# Bandpass-filtered signal: # Bandpass-filtered signal:
signal = data['filt'][:, channel]
ax_full, ax_zoom = axes[0, :] ax_full, ax_zoom = axes[0, :]
c, lw = colors['filt'], linewidths['filt'] plot_line(ax_full, t_full, data['filt'], c=colors['filt'], lw=lw_full['filt'])
ax_full.plot(t_full, signal, c=c, lw=lw) plot_line(ax_zoom, t_zoom, data['filt'][zoom_mask], c=colors['filt'], lw=lw_zoom['filt'])
ax_zoom.plot(t_zoom, signal[zoom_mask], c=c, lw=lw) hide_axis(ax_full, 'bottom')
ax_full.set_ylim(signal.min(), signal.max()) hide_axis(ax_zoom, 'bottom')
hide_axis(ax_zoom, 'left')
# Signal envelope: # Signal envelope:
signal = data['env'][:, channel]
ax_full, ax_zoom = axes[1, :] ax_full, ax_zoom = axes[1, :]
c, lw = colors['env'], linewidths['env'] plot_line(ax_full, t_full, data['env'], ymin=0, c=colors['env'], lw=lw_full['env'])
ax_full.plot(t_full, signal, c=c, lw=lw) plot_line(ax_zoom, t_zoom, data['env'][zoom_mask], ymin=0, c=colors['env'], lw=lw_zoom['env'])
ax_zoom.plot(t_zoom, signal[zoom_mask], c=c, lw=lw) hide_axis(ax_full, 'bottom')
ax_full.set_ylim(0, signal.max()) hide_axis(ax_zoom, 'bottom')
hide_axis(ax_zoom, 'left')
# Logarithmic envelope: # Logarithmic envelope:
signal = data['log'][:, channel]
ax_full, ax_zoom = axes[2, :] ax_full, ax_zoom = axes[2, :]
c, lw = colors['log'], linewidths['log'] plot_line(ax_full, t_full, data['log'], ymax=0, c=colors['log'], lw=lw_full['log'])
ax_full.plot(t_full, signal, c=c, lw=lw) plot_line(ax_zoom, t_zoom, data['log'][zoom_mask], ymax=0, c=colors['log'], lw=lw_zoom['log'])
ax_zoom.plot(t_zoom, signal[zoom_mask], c=c, lw=lw) hide_axis(ax_full, 'bottom')
ax_full.set_ylim(signal.min(), 0) hide_axis(ax_zoom, 'bottom')
hide_axis(ax_zoom, 'left')
# Adapted envelope: # Adapted envelope:
signal = data['inv'][:, channel]
ax_full, ax_zoom = axes[3, :] ax_full, ax_zoom = axes[3, :]
c, lw = colors['inv'], linewidths['inv'] plot_line(ax_full, t_full, data['inv'], c=colors['inv'], lw=lw_full['inv'])
ax_full.plot(t_full, signal, c=c, lw=lw) plot_line(ax_zoom, t_zoom, data['inv'][zoom_mask], c=colors['inv'], lw=lw_zoom['inv'])
ax_zoom.plot(t_zoom, signal[zoom_mask], c=c, lw=lw) hide_axis(ax_zoom, 'left')
ax_full.set_ylim(signal.min(), signal.max())
# Posthoc adjustments: # Posthoc adjustments:
ax_full.set_xlim(t_full[0], t_full[-1]) ax_full.set_xlim(t_full[0], t_full[-1])
ax_zoom.set_xlim(t_zoom[0], t_zoom[-1]) ax_zoom.set_xlim(t_zoom[0], t_zoom[-1])
indicate_zoom(fig, axes[0, 0], axes[-1, 0], zoom_abs, **zoom_kwargs)
indicate_zoom(fig, axes[0, 1], axes[-1, 1], zoom_abs, **zoom_kwargs)
if save_name is not None:
fig.savefig(f'{save_name}_pre.pdf')
# PART II: FEATURE EXTRACTION STAGE: # PART II: FEATURE EXTRACTION STAGE:
fig, axes = plt.subplots(3, 2, **fig_kwargs) fig, axes = prepare_fig(3, 2, **fig_kwargs, **grid_kwargs)
fig.supylabel('amplitude', fontsize=plt.rcParams['axes.labelsize']) super_xlabel('time [s]', fig, axes[0, 0], axes[0, -1])
fig.supxlabel('time [s]', fontsize=plt.rcParams['axes.labelsize']) super_ylabel('amplitude', fig, axes[0, 0], axes[-1, 0])
# Convolutional filter responses: # Convolutional filter responses:
signal = data['conv'][:, :, channel]
ax_full, ax_zoom = axes[0, :] ax_full, ax_zoom = axes[0, :]
c, lw = colors['conv'], linewidths['conv'] plot_line(ax_full, t_full, data['conv'], c=colors['conv'], lw=lw_full['conv'])
ax_full.plot(t_full, signal, c=c, lw=lw) plot_line(ax_zoom, t_zoom, data['conv'][zoom_mask, :], c=colors['conv'], lw=lw_zoom['conv'])
ax_zoom.plot(t_zoom, signal[zoom_mask, :], c=c, lw=lw) hide_axis(ax_full, 'bottom')
ax_full.set_ylim(signal.min(), signal.max()) hide_axis(ax_zoom, 'bottom')
hide_axis(ax_zoom, 'left')
# Binary responses: # Binary responses:
signal = data['bi'][:, :, channel]
ax_full, ax_zoom = axes[1, :] ax_full, ax_zoom = axes[1, :]
c, lw = colors['bi'], linewidths['bi'] plot_barcode(ax_full, t_full, data['bi'], color=colors['bi'])
ax_full.plot(t_full, signal, c=c, lw=lw) plot_barcode(ax_zoom, t_zoom, data['bi'][zoom_mask, :], color=colors['bi'])
ax_zoom.plot(t_zoom, signal[zoom_mask, :], c=c, lw=lw)
ax_full.set_ylim(signal.min(), signal.max())
# Finalized features: # Finalized features:
signal = data['feat'][:, :, channel]
ax_full, ax_zoom = axes[2, :] ax_full, ax_zoom = axes[2, :]
c, lw = colors['feat'], linewidths['feat'] plot_line(ax_full, t_full, data['feat'], ymin=0, ymax=1, c=colors['feat'], lw=lw_full['feat'])
ax_full.plot(t_full, signal, c=c, lw=lw) plot_line(ax_zoom, t_zoom, data['feat'][zoom_mask, :], ymin=0, ymax=1, c=colors['feat'], lw=lw_zoom['feat'])
ax_zoom.plot(t_zoom, signal[zoom_mask, :], c=c, lw=lw) hide_axis(ax_zoom, 'left')
ax_full.set_ylim(0, 1)
# Posthoc adjustments: # Posthoc adjustments:
ax_full.set_xlim(t_full[0], t_full[-1]) ax_full.set_xlim(t_full[0], t_full[-1])
ax_zoom.set_xlim(t_zoom[0], t_zoom[-1]) ax_zoom.set_xlim(t_zoom[0], t_zoom[-1])
indicate_zoom(fig, axes[0, 0], axes[-1, 0], zoom_abs, **zoom_kwargs)
indicate_zoom(fig, axes[0, 1], axes[-1, 1], zoom_abs, **zoom_kwargs)
if save_name is not None:
fig.savefig(f'{save_name}_feat.pdf')
plt.show() plt.show()

20
python/plotstyle_plt.py
View File

@ -8,15 +8,18 @@ mpl.rcParams['font.style'] = 'normal'
mpl.rcParams['font.family'] = 'serif' mpl.rcParams['font.family'] = 'serif'
mpl.rcParams['mathtext.fontset'] = 'cm' mpl.rcParams['mathtext.fontset'] = 'cm'
mpl.rcParams['mathtext.default'] = 'regular' mpl.rcParams['mathtext.default'] = 'regular'
# Font sizes: # Font sizes:
mpl.rcParams['font.size'] = 14 mpl.rcParams['font.size'] = 14
mpl.rcParams['figure.titlesize'] = 15 mpl.rcParams['figure.titlesize'] = 15
mpl.rcParams['figure.labelsize'] = 14
mpl.rcParams['axes.labelsize'] = 14 mpl.rcParams['axes.labelsize'] = 14
mpl.rcParams['axes.titlesize'] = 14 mpl.rcParams['axes.titlesize'] = 14
mpl.rcParams['xtick.labelsize'] = 13 mpl.rcParams['xtick.labelsize'] = 13
mpl.rcParams['ytick.labelsize'] = 13 mpl.rcParams['ytick.labelsize'] = 13
mpl.rcParams['legend.fontsize'] = 14 mpl.rcParams['legend.fontsize'] = 14
mpl.rcParams['legend.title_fontsize'] = 14 mpl.rcParams['legend.title_fontsize'] = 14
# Font weights: # Font weights:
single_weight = ['normal', 'bold'][0] single_weight = ['normal', 'bold'][0]
mpl.rcParams['font.weight'] = single_weight mpl.rcParams['font.weight'] = single_weight
@ -32,6 +35,7 @@ mpl.rcParams['figure.raise_window'] = True
# mpl.rcParams['savefig.dpi'] = 500 # mpl.rcParams['savefig.dpi'] = 500
# Axes parameters: # Axes parameters:
mpl.rcParams['axes.linewidth'] = 1.5
mpl.rcParams['axes.spines.top'] = False mpl.rcParams['axes.spines.top'] = False
mpl.rcParams['axes.spines.right'] = False mpl.rcParams['axes.spines.right'] = False
mpl.rcParams['axes.xmargin'] = 0 mpl.rcParams['axes.xmargin'] = 0
@ -39,9 +43,19 @@ mpl.rcParams['axes.ymargin'] = 0
mpl.rcParams['axes.autolimit_mode'] = 'round_numbers' mpl.rcParams['axes.autolimit_mode'] = 'round_numbers'
mpl.rcParams['axes.labelpad'] = 3 mpl.rcParams['axes.labelpad'] = 3
# Tick parameters: # Major tick parameters:
mpl.rcParams['xtick.major.pad'] = 5 mpl.rcParams['xtick.major.size'] = 5
mpl.rcParams['ytick.major.pad'] = 5 mpl.rcParams['xtick.major.width'] = 1.5
mpl.rcParams['xtick.major.pad'] = 3.5
mpl.rcParams['ytick.major.size'] = 5
mpl.rcParams['ytick.major.width'] = 1.5
mpl.rcParams['ytick.major.pad'] = 3.5
# Minor tick parameters:
mpl.rcParams['xtick.minor.size'] = 2
mpl.rcParams['xtick.minor.width'] = 1
mpl.rcParams['ytick.minor.size'] = 2
mpl.rcParams['ytick.minor.width'] = 1
# Legend parameters: # Legend parameters:
mpl.rcParams['legend.frameon'] = False mpl.rcParams['legend.frameon'] = False

61
python/save_snippet_data.py Normal file
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@ -0,0 +1,61 @@
import numpy as np
from thunderhopper.filetools import search_files, crop_paths
from thunderhopper.model import configuration, process_signal
from thunderhopper.modeltools import load_data
from IPython import embed
## SETTINGS:
# General:
overwrite = True
input_folder = '../data/raw/'
output_folder = '../data/processed/'
stages = ['raw', 'filt', 'env', 'log', 'inv', 'conv', 'bi', 'feat', 'norm']
if True:
# Overwrites edited:
stages.append('songs')
# Interactivity:
reload_saved = False
gui = False
# Processing:
env_rate = 44100.0
feat_rate = 44100.0
sigmas = [0.001, 0.002, 0.004, 0.008, 0.016, 0.032]
types = [1, -1, 2, -2, 3, -3, 4, -4, 5, -5,
6, -6, 7, -7, 8, -8, 9, -9, 10, -10]
config = configuration(env_rate, feat_rate, types=types, sigmas=sigmas)
config.update({
'channel': 0,
'rate_ratio': None,
'env_fcut': 250,
'inv_fcut': 5,
'feat_thresh': np.load('../data/kernel_thresholds.npy') * 0.1,
'feat_fcut': 0.5,
'label_channels': 0,
'label_thresh': 0.5,
})
## PREPARATION:
# Fetch WAV recording files:
input_paths = search_files(ext='wav', dir=input_folder)
path_names = crop_paths(input_paths)
# PROCESSING:
# Run processing pipeline:
for path, name in zip(input_paths, path_names):
print('Processing:', name)
# Fetch and store representations:
save = None if output_folder is None else output_folder + f'{name}.npz'
process_signal(config, stages, path, save=save,
label_edit=gui, overwrite=overwrite)
# Cross-control:
if reload_saved:
data, params = load_data(save, stages, ['songs', 'noise'])
embed()
print('Done.')

195
python/save_stage_colors.py Normal file
View File

@ -0,0 +1,195 @@
import numpy as np
import matplotlib.pyplot as plt
from tkinter.colorchooser import askcolor
from IPython import embed
def is_hex_color(color):
if isinstance(color, str) and color.startswith('#') and len(color) == 7:
try:
int(color[1:], 16)
return True
except ValueError:
return False
return False
def is_rgb_color(color):
if isinstance(color, (tuple, list)) and len(color) == 3:
return all(isinstance(c, int) and 0 <= c <= 255 for c in color)
return False
def hex_to_rgb(color):
color = color.lstrip('#')
return tuple(int(color[i:i+2], 16) for i in (0, 2, 4))
def rgb_to_hex(color):
return '#{:02x}{:02x}{:02x}'.format(*color)
def whiten_color(color, factors):
is_hex = is_hex_color(color)
if is_hex:
color = hex_to_rgb(color)
elif not is_rgb_color(color):
raise ValueError('Color format must be hex string or RGB tuple.')
whitened = tuple(min(255, int(c + (255 - c) * f)) for c, f in zip(color, factors))
return rgb_to_hex(whitened) if is_hex else whitened
def color_selector(n=5, colors=None, save=None, labels=None, hex=True,
back_color='w', edge_color='k', edge_width=2):
def pick_color(color='#ffffff', hex=True):
color = askcolor(initialcolor=color)[hex]
return color
def update_color(artists, color):
for i, artist in enumerate(artists):
if isinstance(artist, plt.Rectangle):
# Update patch colors:
artist.set_fc(color)
if i in [0, 1]:
artist.set_ec(color)
elif isinstance(artist, plt.Line2D):
# Update marker colors:
artist.set_mfc(color)
if i in [0, 1]:
artist.set_mec(color)
fig.canvas.draw()
return None
# Prepare colors:
if colors is None:
colors = ['#ffffff' for _ in range(n)]
start_colors = colors.copy()
n = len(colors)
plt.ion()
# Prepare graphical interface:
fig, ax = plt.subplots(figsize=(10, 2), layout='constrained')
ax.set_facecolor(back_color)
ax.set_xlim(0, n)
ax.set_ylim(0, 4)
ax.axis('off')
# Add different color indicators:
artist_groups, group_inds = {}, {}
for i, color in enumerate(colors):
# Color on background, uniform edge:
p1 = ax.add_patch(plt.Rectangle((i, 0), 1, 1, fc=color, ec=color))
l1 = ax.plot(i + 0.5, 1.5, marker='o', ms=20, mfc=color, mec=color)[0]
# Color on background, black edge:
p2 = ax.add_patch(plt.Rectangle((i, 3), 1, 1, fc=color, ec=edge_color, lw=edge_width))
l2 = ax.plot(i + 0.5, 2.5, marker='o', ms=20, mfc=color, mec=edge_color, mew=edge_width)[0]
# Update artist mappings:
handles = [p1, l1, l2, p2]
artist_groups[i] = handles
for handle in handles:
handle.set_picker(True)
group_inds[handle] = i
# Initialize memory variables for avoiding assignments:
swap_groups, swap_colors = [None, None], [None, None]
focus_group, focus_color = [None], [None, None]
# Interactivity:
def on_key(event):
# Abort and retry:
if event.key == 'q':
print('\nRestarting with original settings...')
plt.close(fig)
return color_selector(n, start_colors, save, labels, hex,
back_color, edge_color, edge_width)
# Exit without saving:
elif event.key == 'escape':
print('\nExiting without saving...')
plt.close(fig)
return None
# Accept and save colors to file:
elif event.key == 'enter' and save is not None:
if labels is not None:
# Convert to file dictionary and write to npz file:
data = {str(label): col for label, col in zip(labels, colors)}
np.savez(f'{save}.npz', **data)
else:
# Write array (n, 3) or (n,) to npy file:
np.save(f'{save}.npy', np.array(colors))
print(f'\nSaved {n} colors to file: {save}')
plt.close(fig)
return None
def on_pick(event):
# Pick color for chosen group:
if event.mouseevent.button == 1:
# Update memory variables:
focus_group[0] = group_inds[event.artist]
focus_color[0] = colors[focus_group[0]]
# Trigger color picker dialogue:
focus_color[1] = pick_color(focus_color[0], hex)
if focus_color[1] is not None:
# Apply, update, and report only if dialogue was not cancelled:
update_color(artist_groups[focus_group[0]], focus_color[1])
colors[focus_group[0]] = focus_color[1]
print(f'\nUpdated color {focus_group[0] + 1} / {n}: {focus_color[1]}')
# Select 1st color to swap:
elif event.mouseevent.button == 3:
# Update memory variables and report:
swap_groups[0] = group_inds[event.artist]
swap_colors[0] = colors[swap_groups[0]]
print(f'\nSelected 1st swap color: {swap_groups[0] + 1} / {n}')
# Select 2nd color to swap and execute:
elif swap_groups[0] is not None and event.mouseevent.button == 2:
# Update memory variables and report:
swap_groups[1] = group_inds[event.artist]
swap_colors[1] = colors[swap_groups[1]]
print(f'Selected 2nd swap color: {swap_groups[1] + 1} / {n}')
print(f'Swapping colors: {swap_groups[0] + 1} <-> {swap_groups[1] + 1}')
# Swap colors:
for i in [0, 1]:
# Apply to artist group and update global color list:
update_color(artist_groups[swap_groups[i]], swap_colors[1 - i])
colors[swap_groups[i]] = swap_colors[1 - i]
# Reset memory variables:
swap_groups[0], swap_groups[1] = None, None
swap_colors[0], swap_colors[1] = None, None
# Establish interactivity:
plt.connect('key_press_event', on_key)
plt.connect('pick_event', on_pick)
plt.ioff()
return colors
# Settings:
stages = ['filt', 'env', 'log', 'inv', 'conv', 'bi', 'feat']
file_name = None#'../data/stage_colors'
colors = None
if True:
colors = dict(np.load('../data/stage_colors.npz'))
colors = [colors[stage].item() for stage in colors.keys()]
# Execution:
colors = color_selector(len(stages), colors, save=file_name, labels=stages, hex=True)
plt.show()
embed()