Built color selection infrastructure and assigned stage-specific colors (WIP).
Added 2 plots to methods (WIP).
This commit is contained in:
j-hartling
parent
d78dcf4f4a
commit
49b2bdcfca
8
.gitignore
vendored
8
.gitignore
vendored
@ -1,2 +1,6 @@
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data/*
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./__pycache__/
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# Python:
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./__pycache__/
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*.py[cod]
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*$py.class
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# Recording data:
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data/*
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BIN
figures/pathway_stages_feat.pdf
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BIN
figures/pathway_stages_feat.pdf
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BIN
figures/pathway_stages_pre.pdf
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BIN
figures/pathway_stages_pre.pdf
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32
main.aux
32
main.aux
@ -222,7 +222,9 @@
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\abx@aux@page{68}{7}
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\abx@aux@page{69}{7}
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\newlabel{eq:highpass}{{4}{7}{}{}{}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {2.2}Feature extraction by individual neurons}{7}{}\protected@file@percent }
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\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces \relax }}{8}{}\protected@file@percent }
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\newlabel{fig:pre}{{2}{8}{}{}{}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {2.2}Feature extraction by individual neurons}{8}{}\protected@file@percent }
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\newlabel{eq:conv}{{5}{8}{}{}{}}
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\newlabel{eq:gabor}{{6}{8}{}{}{}}
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\abx@aux@cite{0}{ronacher1986routes}
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@ -237,23 +239,25 @@
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\abx@aux@page{70}{9}
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\abx@aux@page{71}{9}
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\abx@aux@page{72}{9}
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\newlabel{eq:lowpass}{{10}{9}{}{}{}}
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\@writefile{toc}{\contentsline {section}{\numberline {3}Two mechanisms driving the emergence of intensity-invariant song representation}{9}{}\protected@file@percent }
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\newlabel{eq:lowpass}{{10}{10}{}{}{}}
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\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces \relax }}{10}{}\protected@file@percent }
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\newlabel{fig:stages_feat}{{3}{10}{}{}{}}
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\@writefile{toc}{\contentsline {section}{\numberline {3}Two mechanisms driving the emergence of intensity-invariant song representation}{10}{}\protected@file@percent }
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\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Logarithmic scaling \& spike-frequency adaptation}{10}{}\protected@file@percent }
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\newlabel{eq:toy_env}{{11}{10}{}{}{}}
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\newlabel{eq:toy_snr}{{12}{10}{}{}{}}
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\newlabel{eq:toy_log}{{13}{10}{}{}{}}
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\newlabel{eq:toy_env}{{11}{11}{}{}{}}
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\newlabel{eq:toy_snr}{{12}{11}{}{}{}}
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\newlabel{eq:toy_log}{{13}{11}{}{}{}}
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\newlabel{eq:toy_highpass}{{14}{11}{}{}{}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Threshold nonlinearity \& temporal averaging}{11}{}\protected@file@percent }
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\newlabel{eq:pdf_split}{{15}{11}{}{}{}}
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\newlabel{eq:pdf}{{16}{11}{}{}{}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Threshold nonlinearity \& temporal averaging}{12}{}\protected@file@percent }
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\newlabel{eq:pdf_split}{{15}{12}{}{}{}}
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\newlabel{eq:pdf}{{16}{12}{}{}{}}
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\newlabel{eq:feat_avg}{{17}{12}{}{}{}}
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\newlabel{eq:feat_prop}{{18}{12}{}{}{}}
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\newlabel{eq:feat_prop}{{18}{13}{}{}{}}
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\abx@aux@cite{0}{stumpner1991auditory}
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\abx@aux@segm{0}{0}{stumpner1991auditory}
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\@writefile{toc}{\contentsline {section}{\numberline {4}Discriminating species-specific song\\patterns in feature space}{13}{}\protected@file@percent }
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\@writefile{toc}{\contentsline {section}{\numberline {5}Conclusions \& outlook}{13}{}\protected@file@percent }
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\abx@aux@page{73}{13}
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\@writefile{toc}{\contentsline {section}{\numberline {4}Discriminating species-specific song\\patterns in feature space}{14}{}\protected@file@percent }
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\@writefile{toc}{\contentsline {section}{\numberline {5}Conclusions \& outlook}{14}{}\protected@file@percent }
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\abx@aux@page{73}{14}
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\gdef\svg@ink@ver@settings{{\m@ne }{inkscape}{\m@ne }}
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\abx@aux@read@bbl@mdfivesum{1380DC8C93D2855FDB132CC5A40AD52F}
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\gdef \@abspage@last{13}
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\gdef \@abspage@last{14}
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@ -1951,19 +1951,19 @@
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\range{pages}{10}
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\endentry
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\entry{stumpner1994song}{article}{}
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\name{author}{2}{}{%
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\name{author}{2}{ul=2}{%
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{{un=0,uniquepart=base,hash=a7bef35fb61ea64e0f04d6c87e5aa622}{%
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family={Stumpner},
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familyi={S\bibinitperiod},
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given={Andreas},
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giveni={A\bibinitperiod},
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givenun=0}}%
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{{un=0,uniquepart=base,hash=ecb958a09c71420bd1e10f3fee8c24ac}{%
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{{un=1,uniquepart=given,hash=ecb958a09c71420bd1e10f3fee8c24ac}{%
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family={Helversen},
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familyi={H\bibinitperiod},
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given={Otto},
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giveni={O\bibinitperiod},
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givenun=0,
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givenun=1,
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prefix={von},
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prefixi={v\bibinitperiod},
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prefixun=0}}%
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@ -1987,6 +1987,44 @@
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\field{pages}{1\bibrangedash 23}
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\range{pages}{23}
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\endentry
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\entry{stumpner1991auditory}{article}{}
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\name{author}{2}{ul=2}{%
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{{un=0,uniquepart=base,hash=a7bef35fb61ea64e0f04d6c87e5aa622}{%
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family={Stumpner},
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familyi={S\bibinitperiod},
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given={Andreas},
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giveni={A\bibinitperiod},
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givenun=0}}%
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{{un=0,uniquepart=base,hash=4ce9349f95ced7a4831a5efa0fe5b00f}{%
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family={Ronacher},
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familyi={R\bibinitperiod},
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given={Bernhard},
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giveni={B\bibinitperiod},
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givenun=0}}%
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}
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\list{publisher}{1}{%
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{The Company of Biologists Ltd}%
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}
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\strng{namehash}{c6b9dac84d9d74ba87037123f4e21034}
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\strng{fullhash}{c6b9dac84d9d74ba87037123f4e21034}
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\strng{bibnamehash}{c6b9dac84d9d74ba87037123f4e21034}
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\strng{authorbibnamehash}{c6b9dac84d9d74ba87037123f4e21034}
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\strng{authornamehash}{c6b9dac84d9d74ba87037123f4e21034}
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\strng{authorfullhash}{c6b9dac84d9d74ba87037123f4e21034}
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\field{sortinit}{S}
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\field{sortinithash}{b164b07b29984b41daf1e85279fbc5ab}
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\field{extradatescope}{labelyear}
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\field{labeldatesource}{}
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\field{labelnamesource}{author}
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\field{labeltitlesource}{title}
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\field{journaltitle}{Journal of Experimental Biology}
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\field{number}{1}
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\field{title}{Auditory interneurones in the metathoracic ganglion of the grasshopper Chorthippus biguttulus: I. Morphological and physiological characterization}
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\field{volume}{158}
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\field{year}{1991}
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\field{pages}{391\bibrangedash 410}
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\range{pages}{20}
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\endentry
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\entry{suga1960peripheral}{article}{}
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\name{author}{1}{}{%
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{{un=0,uniquepart=base,hash=cb8492490b7b1d1c021ccd740577eab6}{%
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main.blg
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main.blg
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[0] Config.pm:307> INFO - This is Biber 2.19
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[35] biber:340> INFO - === Do Feb 12, 2026, 15:55:36
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[71] Biber.pm:979> INFO - Found 55 citekeys in bib section 0
|
||||
[76] Biber.pm:4419> INFO - Processing section 0
|
||||
[80] Biber.pm:4610> INFO - Looking for bibtex file 'cite.bib' for section 0
|
||||
[82] bibtex.pm:1713> INFO - LaTeX decoding ...
|
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[111] bibtex.pm:1519> INFO - Found BibTeX data source 'cite.bib'
|
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[277] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
|
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[277] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
|
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[277] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
|
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[277] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
|
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[299] bbl.pm:660> INFO - Writing 'main.bbl' with encoding 'UTF-8'
|
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[310] bbl.pm:763> INFO - Output to main.bbl
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 21, 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
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 58, 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
|
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[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 91, 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
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 118, 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
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 157, 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
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 196, 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
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 229, 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
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 258, 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
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 289, 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
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 328, 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
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 419, warning: 6 characters of junk seen at toplevel
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 428, warning: 6 characters of junk seen at toplevel
|
||||
[310] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 437, warning: 6 characters of junk seen at toplevel
|
||||
[311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 456, 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
|
||||
[311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 535, 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
|
||||
[311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 576, 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
|
||||
[311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 648, 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
|
||||
[311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 688, 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
|
||||
[311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 729, 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
|
||||
[311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.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 775, 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
|
||||
[311] Biber.pm:131> WARN - BibTeX subsystem: /tmp/biber_tmp_6HUw/347c261ec4135a5723bef5c751f5078f_117857.utf8, line 817, warning: 6 characters of junk seen at toplevel
|
||||
[311] Biber.pm:133> INFO - WARNINGS: 55
|
||||
|
||||
@ -1,14 +1,14 @@
|
||||
# Fdb version 4
|
||||
["biber main"] 1770908135.92672 "main.bcf" "main.bbl" "main" 1770909740.85496 0
|
||||
["biber main"] 1771341035.4003 "main.bcf" "main.bbl" "main" 1771341094.70787 0
|
||||
"cite.bib" 1770904753.08918 27483 4290db0c91f7b5055e25472ef913f6b4 ""
|
||||
"main.bcf" 1770909740.80982 112931 2a478116d80ebb1ada7083a24facd6e3 "pdflatex"
|
||||
"main.bcf" 1771341094.52472 112931 2a478116d80ebb1ada7083a24facd6e3 "pdflatex"
|
||||
(generated)
|
||||
"main.bbl"
|
||||
"main.blg"
|
||||
(rewritten before read)
|
||||
["pdflatex"] 1770909740.04415 "/home/hartling/phd/paper/paper_2025/main.tex" "main.pdf" "main" 1770909740.85516 0
|
||||
["pdflatex"] 1771341093.48122 "/home/hartling/phd/paper/paper_2025/main.tex" "main.pdf" "main" 1771341094.7081 0
|
||||
"/etc/texmf/web2c/texmf.cnf" 1761560044.43676 475 c0e671620eb5563b2130f56340a5fde8 ""
|
||||
"/home/hartling/phd/paper/paper_2025/main.tex" 1770909739.95483 39127 a7cd2ca5121e6f89fb995bfcbb00bb76 ""
|
||||
"/home/hartling/phd/paper/paper_2025/main.tex" 1771341093.40273 39474 270d81ac4d9b5510e0f5b6ffd47d4548 ""
|
||||
"/usr/share/texlive/texmf-dist/fonts/map/fontname/texfonts.map" 1577235249 3524 cb3e574dea2d1052e39280babc910dc8 ""
|
||||
"/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/cmextra/cmex7.tfm" 1246382020 1004 54797486969f23fa377b128694d548df ""
|
||||
"/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/cmextra/cmex8.tfm" 1246382020 988 bdf658c3bfc2d96d3c8b02cfc1c94c20 ""
|
||||
@ -151,10 +151,12 @@
|
||||
"/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1761648508 8213325 7fd20752ab46ff9aa583e4973d7433df ""
|
||||
"figures/fig_auditory_pathway.pdf" 1769682029.31297 1284536 cd071429286586e390a99d74f742d2d5 ""
|
||||
"figures/fig_auditory_pathway.pdf_tex" 1769682029.31397 2624 f8d79af301f26c4639670ba4283887a2 ""
|
||||
"main.aux" 1770909740.80382 10828 27979d381c53a50541bc62175148bf97 "pdflatex"
|
||||
"main.bbl" 1770908136.51937 91039 1380dc8c93d2855fdb132cc5a40ad52f "biber main"
|
||||
"main.run.xml" 1770909740.80982 2335 a049bc26a7f032e842ce55de5bc38328 "pdflatex"
|
||||
"main.tex" 1770909739.95483 39127 a7cd2ca5121e6f89fb995bfcbb00bb76 ""
|
||||
"figures/pathway_stages_feat.pdf" 1771340650.40761 82316897 05ba2bb6e8749f206ed48a1452e502fe ""
|
||||
"figures/pathway_stages_pre.pdf" 1771340634.77974 417332 f29087bfa1db0ef1a7ad1c27dc1875b2 ""
|
||||
"main.aux" 1771341094.51872 11126 896020d94c8241fd7543e4bc1dff8f68 "pdflatex"
|
||||
"main.bbl" 1771341036.00124 91039 1380dc8c93d2855fdb132cc5a40ad52f "biber main"
|
||||
"main.run.xml" 1771341094.52472 2335 a049bc26a7f032e842ce55de5bc38328 "pdflatex"
|
||||
"main.tex" 1771341093.40273 39474 270d81ac4d9b5510e0f5b6ffd47d4548 ""
|
||||
(generated)
|
||||
"main.aux"
|
||||
"main.bcf"
|
||||
|
||||
10
main.fls
10
main.fls
@ -275,11 +275,21 @@ INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmbx12.tfm
|
||||
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmr10.tfm
|
||||
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmbx10.tfm
|
||||
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmbx12.tfm
|
||||
INPUT ./figures/pathway_stages_pre.pdf
|
||||
INPUT ./figures/pathway_stages_pre.pdf
|
||||
INPUT ./figures/pathway_stages_pre.pdf
|
||||
INPUT ./figures/pathway_stages_pre.pdf
|
||||
INPUT ./figures/pathway_stages_pre.pdf
|
||||
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmmi10.tfm
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||||
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmsy10.tfm
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||||
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmex10.tfm
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||||
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam10.tfm
|
||||
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm10.tfm
|
||||
INPUT ./figures/pathway_stages_feat.pdf
|
||||
INPUT ./figures/pathway_stages_feat.pdf
|
||||
INPUT ./figures/pathway_stages_feat.pdf
|
||||
INPUT ./figures/pathway_stages_feat.pdf
|
||||
INPUT ./figures/pathway_stages_feat.pdf
|
||||
INPUT main.aux
|
||||
INPUT main.run.xml
|
||||
OUTPUT main.run.xml
|
||||
|
||||
33
main.log
33
main.log
@ -1,4 +1,4 @@
|
||||
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex 2025.10.28) 12 FEB 2026 16:22
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||||
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex 2025.10.28) 17 FEB 2026 16:11
|
||||
entering extended mode
|
||||
restricted \write18 enabled.
|
||||
file:line:error style messages enabled.
|
||||
@ -773,12 +773,23 @@ Overfull \hbox (4.40714pt too wide) in paragraph at lines 393--402
|
||||
\OT1/cmr/m/n/12 the sub-se-quent lo-cal in-terneu-rons ([]; [])
|
||||
[]
|
||||
|
||||
[7] [8]
|
||||
Overfull \hbox (9.43962pt too wide) in paragraph at lines 511--511
|
||||
<figures/pathway_stages_pre.pdf, id=1008, 910.48819pt x 341.43306pt>
|
||||
File: figures/pathway_stages_pre.pdf Graphic file (type pdf)
|
||||
<use figures/pathway_stages_pre.pdf>
|
||||
Package pdftex.def Info: figures/pathway_stages_pre.pdf used on input line 414.
|
||||
(pdftex.def) Requested size: 455.24411pt x 170.7161pt.
|
||||
[7] [8 <./figures/pathway_stages_pre.pdf>] [9]
|
||||
<figures/pathway_stages_feat.pdf, id=1058, 910.48819pt x 341.43306pt>
|
||||
File: figures/pathway_stages_feat.pdf Graphic file (type pdf)
|
||||
<use figures/pathway_stages_feat.pdf>
|
||||
Package pdftex.def Info: figures/pathway_stages_feat.pdf used on input line 521.
|
||||
(pdftex.def) Requested size: 455.24411pt x 170.7161pt.
|
||||
|
||||
Overfull \hbox (9.43962pt too wide) in paragraph at lines 527--527
|
||||
[]\OT1/cmr/bx/n/17.28 Two mech-a-nisms driv-ing the emer-gence of intensity-
|
||||
[]
|
||||
|
||||
[9] [10] [11] [12] [13] (./main.aux)
|
||||
[10 <./figures/pathway_stages_feat.pdf>] [11] [12] [13] [14] (./main.aux)
|
||||
***********
|
||||
LaTeX2e <2023-11-01> patch level 1
|
||||
L3 programming layer <2024-01-22>
|
||||
@ -788,18 +799,18 @@ Package logreq Info: Writing requests to 'main.run.xml'.
|
||||
|
||||
)
|
||||
Here is how much of TeX's memory you used:
|
||||
20711 strings out of 474222
|
||||
446040 string characters out of 5748732
|
||||
20727 strings out of 474222
|
||||
446637 string characters out of 5748732
|
||||
1937975 words of memory out of 5000000
|
||||
42696 multiletter control sequences out of 15000+600000
|
||||
42712 multiletter control sequences out of 15000+600000
|
||||
569035 words of font info for 78 fonts, out of 8000000 for 9000
|
||||
1143 hyphenation exceptions out of 8191
|
||||
94i,19n,93p,955b,1732s stack positions out of 10000i,1000n,20000p,200000b,200000s
|
||||
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/symbols/msbm10.pfb>
|
||||
Output written on main.pdf (13 pages, 1450935 bytes).
|
||||
Output written on main.pdf (14 pages, 84180383 bytes).
|
||||
PDF statistics:
|
||||
1109 PDF objects out of 1200 (max. 8388607)
|
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702 compressed objects within 8 object streams
|
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1172 PDF objects out of 1200 (max. 8388607)
|
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714 compressed objects within 8 object streams
|
||||
0 named destinations out of 1000 (max. 500000)
|
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18 words of extra memory for PDF output out of 10000 (max. 10000000)
|
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28 words of extra memory for PDF output out of 10000 (max. 10000000)
|
||||
|
||||
|
||||
BIN
main.synctex.gz
BIN
main.synctex.gz
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16
main.tex
16
main.tex
@ -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
|
||||
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}
|
||||
|
||||
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
|
||||
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}
|
||||
|
||||
\textbf{Definition of invariance (general, systemic):}\\
|
||||
|
||||
@ -1,34 +1,123 @@
|
||||
import glob
|
||||
import plotstyle_plt
|
||||
import glob
|
||||
import numpy as np
|
||||
import matplotlib.pyplot as plt
|
||||
from itertools import product
|
||||
from thunderhopper.modeltools import load_data
|
||||
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:
|
||||
data_paths = glob.glob('../data/processed/*.npz')
|
||||
stages = ['filt', 'env', 'log', 'inv',
|
||||
'conv', 'bi', 'feat']
|
||||
channel = 0
|
||||
target = 'Omocestus_rufipes'
|
||||
data_paths = glob.glob(f'../data/processed/{target}*.npz')
|
||||
stages = ['filt', 'env', 'log', 'inv', 'conv', 'bi', 'feat']
|
||||
save_name = '../figures/pathway_stages'
|
||||
|
||||
# PLOT SETTINGS:
|
||||
fig_kwargs = dict(
|
||||
figsize = np.array([16, 9]) * 0.75,
|
||||
layout = 'constrained',
|
||||
sharex = 'col',
|
||||
sharey = 'row'
|
||||
width=16 / 2.54 * 2,
|
||||
height=6 / 2.54 * 2,
|
||||
rheight=2 / 2.54 * 2,
|
||||
)
|
||||
zoom_rel = np.array([0.4, 0.6])
|
||||
colors = dict(
|
||||
filt='k',
|
||||
env='k',
|
||||
log='k',
|
||||
inv='k',
|
||||
conv='k',
|
||||
bi='k',
|
||||
feat='k'
|
||||
grid_kwargs = dict(
|
||||
wspace=0.15,
|
||||
hspace=0.3,
|
||||
left=0.1,
|
||||
right=0.95,
|
||||
bottom=0.1,
|
||||
top=0.95
|
||||
)
|
||||
linewidths = dict(
|
||||
colors = {s: c.item() for s, c in dict(np.load('../data/stage_colors.npz')).items()}
|
||||
lw_full = dict(
|
||||
filt=0.25,
|
||||
env=0.5,
|
||||
log=0.5,
|
||||
@ -37,11 +126,24 @@ linewidths = dict(
|
||||
bi=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:
|
||||
for data_path in data_paths:
|
||||
if 'Gomphocerippus' in data_path:
|
||||
continue
|
||||
print(f'Processing {data_path}')
|
||||
|
||||
# Load overall data:
|
||||
@ -55,79 +157,80 @@ for data_path in data_paths:
|
||||
|
||||
|
||||
# PART I: PREPROCESSING STAGE
|
||||
fig, axes = plt.subplots(4, 2, **fig_kwargs)
|
||||
fig.supylabel('amplitude', fontsize=plt.rcParams['axes.labelsize'])
|
||||
fig.supxlabel('time [s]', fontsize=plt.rcParams['axes.labelsize'])
|
||||
fig, axes = prepare_fig(4, 2, **fig_kwargs, **grid_kwargs)
|
||||
super_xlabel('time [s]', fig, axes[0, 0], axes[0, -1])
|
||||
super_ylabel('amplitude', fig, axes[0, 0], axes[-1, 0])
|
||||
|
||||
# Bandpass-filtered signal:
|
||||
signal = data['filt'][:, channel]
|
||||
ax_full, ax_zoom = axes[0, :]
|
||||
c, lw = colors['filt'], linewidths['filt']
|
||||
ax_full.plot(t_full, signal, c=c, lw=lw)
|
||||
ax_zoom.plot(t_zoom, signal[zoom_mask], c=c, lw=lw)
|
||||
ax_full.set_ylim(signal.min(), signal.max())
|
||||
plot_line(ax_full, t_full, data['filt'], c=colors['filt'], lw=lw_full['filt'])
|
||||
plot_line(ax_zoom, t_zoom, data['filt'][zoom_mask], c=colors['filt'], lw=lw_zoom['filt'])
|
||||
hide_axis(ax_full, 'bottom')
|
||||
hide_axis(ax_zoom, 'bottom')
|
||||
hide_axis(ax_zoom, 'left')
|
||||
|
||||
# Signal envelope:
|
||||
signal = data['env'][:, channel]
|
||||
ax_full, ax_zoom = axes[1, :]
|
||||
c, lw = colors['env'], linewidths['env']
|
||||
ax_full.plot(t_full, signal, c=c, lw=lw)
|
||||
ax_zoom.plot(t_zoom, signal[zoom_mask], c=c, lw=lw)
|
||||
ax_full.set_ylim(0, signal.max())
|
||||
plot_line(ax_full, t_full, data['env'], ymin=0, c=colors['env'], lw=lw_full['env'])
|
||||
plot_line(ax_zoom, t_zoom, data['env'][zoom_mask], ymin=0, c=colors['env'], lw=lw_zoom['env'])
|
||||
hide_axis(ax_full, 'bottom')
|
||||
hide_axis(ax_zoom, 'bottom')
|
||||
hide_axis(ax_zoom, 'left')
|
||||
|
||||
# Logarithmic envelope:
|
||||
signal = data['log'][:, channel]
|
||||
ax_full, ax_zoom = axes[2, :]
|
||||
c, lw = colors['log'], linewidths['log']
|
||||
ax_full.plot(t_full, signal, c=c, lw=lw)
|
||||
ax_zoom.plot(t_zoom, signal[zoom_mask], c=c, lw=lw)
|
||||
ax_full.set_ylim(signal.min(), 0)
|
||||
plot_line(ax_full, t_full, data['log'], ymax=0, c=colors['log'], lw=lw_full['log'])
|
||||
plot_line(ax_zoom, t_zoom, data['log'][zoom_mask], ymax=0, c=colors['log'], lw=lw_zoom['log'])
|
||||
hide_axis(ax_full, 'bottom')
|
||||
hide_axis(ax_zoom, 'bottom')
|
||||
hide_axis(ax_zoom, 'left')
|
||||
|
||||
# Adapted envelope:
|
||||
signal = data['inv'][:, channel]
|
||||
ax_full, ax_zoom = axes[3, :]
|
||||
c, lw = colors['inv'], linewidths['inv']
|
||||
ax_full.plot(t_full, signal, c=c, lw=lw)
|
||||
ax_zoom.plot(t_zoom, signal[zoom_mask], c=c, lw=lw)
|
||||
ax_full.set_ylim(signal.min(), signal.max())
|
||||
plot_line(ax_full, t_full, data['inv'], c=colors['inv'], lw=lw_full['inv'])
|
||||
plot_line(ax_zoom, t_zoom, data['inv'][zoom_mask], c=colors['inv'], lw=lw_zoom['inv'])
|
||||
hide_axis(ax_zoom, 'left')
|
||||
|
||||
# Posthoc adjustments:
|
||||
ax_full.set_xlim(t_full[0], t_full[-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:
|
||||
fig, axes = plt.subplots(3, 2, **fig_kwargs)
|
||||
fig.supylabel('amplitude', fontsize=plt.rcParams['axes.labelsize'])
|
||||
fig.supxlabel('time [s]', fontsize=plt.rcParams['axes.labelsize'])
|
||||
fig, axes = prepare_fig(3, 2, **fig_kwargs, **grid_kwargs)
|
||||
super_xlabel('time [s]', fig, axes[0, 0], axes[0, -1])
|
||||
super_ylabel('amplitude', fig, axes[0, 0], axes[-1, 0])
|
||||
|
||||
# Convolutional filter responses:
|
||||
signal = data['conv'][:, :, channel]
|
||||
ax_full, ax_zoom = axes[0, :]
|
||||
c, lw = colors['conv'], linewidths['conv']
|
||||
ax_full.plot(t_full, signal, c=c, lw=lw)
|
||||
ax_zoom.plot(t_zoom, signal[zoom_mask, :], c=c, lw=lw)
|
||||
ax_full.set_ylim(signal.min(), signal.max())
|
||||
plot_line(ax_full, t_full, data['conv'], c=colors['conv'], lw=lw_full['conv'])
|
||||
plot_line(ax_zoom, t_zoom, data['conv'][zoom_mask, :], c=colors['conv'], lw=lw_zoom['conv'])
|
||||
hide_axis(ax_full, 'bottom')
|
||||
hide_axis(ax_zoom, 'bottom')
|
||||
hide_axis(ax_zoom, 'left')
|
||||
|
||||
# Binary responses:
|
||||
signal = data['bi'][:, :, channel]
|
||||
ax_full, ax_zoom = axes[1, :]
|
||||
c, lw = colors['bi'], linewidths['bi']
|
||||
ax_full.plot(t_full, signal, c=c, lw=lw)
|
||||
ax_zoom.plot(t_zoom, signal[zoom_mask, :], c=c, lw=lw)
|
||||
ax_full.set_ylim(signal.min(), signal.max())
|
||||
plot_barcode(ax_full, t_full, data['bi'], color=colors['bi'])
|
||||
plot_barcode(ax_zoom, t_zoom, data['bi'][zoom_mask, :], color=colors['bi'])
|
||||
|
||||
# Finalized features:
|
||||
signal = data['feat'][:, :, channel]
|
||||
ax_full, ax_zoom = axes[2, :]
|
||||
c, lw = colors['feat'], linewidths['feat']
|
||||
ax_full.plot(t_full, signal, c=c, lw=lw)
|
||||
ax_zoom.plot(t_zoom, signal[zoom_mask, :], c=c, lw=lw)
|
||||
ax_full.set_ylim(0, 1)
|
||||
plot_line(ax_full, t_full, data['feat'], ymin=0, ymax=1, c=colors['feat'], lw=lw_full['feat'])
|
||||
plot_line(ax_zoom, t_zoom, data['feat'][zoom_mask, :], ymin=0, ymax=1, c=colors['feat'], lw=lw_zoom['feat'])
|
||||
hide_axis(ax_zoom, 'left')
|
||||
|
||||
# Posthoc adjustments:
|
||||
ax_full.set_xlim(t_full[0], t_full[-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()
|
||||
|
||||
|
||||
|
||||
@ -8,15 +8,18 @@ mpl.rcParams['font.style'] = 'normal'
|
||||
mpl.rcParams['font.family'] = 'serif'
|
||||
mpl.rcParams['mathtext.fontset'] = 'cm'
|
||||
mpl.rcParams['mathtext.default'] = 'regular'
|
||||
|
||||
# Font sizes:
|
||||
mpl.rcParams['font.size'] = 14
|
||||
mpl.rcParams['figure.titlesize'] = 15
|
||||
mpl.rcParams['figure.labelsize'] = 14
|
||||
mpl.rcParams['axes.labelsize'] = 14
|
||||
mpl.rcParams['axes.titlesize'] = 14
|
||||
mpl.rcParams['xtick.labelsize'] = 13
|
||||
mpl.rcParams['ytick.labelsize'] = 13
|
||||
mpl.rcParams['legend.fontsize'] = 14
|
||||
mpl.rcParams['legend.title_fontsize'] = 14
|
||||
|
||||
# Font weights:
|
||||
single_weight = ['normal', 'bold'][0]
|
||||
mpl.rcParams['font.weight'] = single_weight
|
||||
@ -32,6 +35,7 @@ mpl.rcParams['figure.raise_window'] = True
|
||||
# mpl.rcParams['savefig.dpi'] = 500
|
||||
|
||||
# Axes parameters:
|
||||
mpl.rcParams['axes.linewidth'] = 1.5
|
||||
mpl.rcParams['axes.spines.top'] = False
|
||||
mpl.rcParams['axes.spines.right'] = False
|
||||
mpl.rcParams['axes.xmargin'] = 0
|
||||
@ -39,10 +43,20 @@ mpl.rcParams['axes.ymargin'] = 0
|
||||
mpl.rcParams['axes.autolimit_mode'] = 'round_numbers'
|
||||
mpl.rcParams['axes.labelpad'] = 3
|
||||
|
||||
# Tick parameters:
|
||||
mpl.rcParams['xtick.major.pad'] = 5
|
||||
mpl.rcParams['ytick.major.pad'] = 5
|
||||
# Major tick parameters:
|
||||
mpl.rcParams['xtick.major.size'] = 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:
|
||||
mpl.rcParams['legend.frameon'] = False
|
||||
mpl.rcParams['legend.scatterpoints'] = 3
|
||||
mpl.rcParams['legend.scatterpoints'] = 3
|
||||
|
||||
61
python/save_snippet_data.py
Normal file
61
python/save_snippet_data.py
Normal file
@ -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
195
python/save_stage_colors.py
Normal 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()
|
||||
Loading…
Reference in New Issue
Block a user