init lab bin

dim

@@ -0,0 +1,3 @@
+#!/bin/bash
+sudo tee /sys/class/backlight/acpi_video0/brightness <<< $1
+

dimk

@@ -0,0 +1,3 @@
+#!/bin/bash
+sudo tee /sys/class/leds/smc::kbd_backlight/brightness <<< $1
+

dimr

@@ -0,0 +1,3 @@
+#!/bin/bash
+redshift -l 38:-122 -t 5500:3500 -g 0.8 -v 
+

hdmi.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#setup external hdmi display if connected, else ensure the display is off
+intern=eDP1
+extern=HDMI1
+
+if xrandr | grep "$extern connected"; then
+    xrandr --output "$intern" --auto --output "$extern" --auto --right-of "$intern"
+else
+    xrandr --output "$intern" --auto --output "$extern" --off
+fi

mv2figs.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+#mv2figs: used by the <cmd-z> screenshot shortcut set in .config/i3/config
+
+#default image location
+blobFolder=$HOME/figures
+
+mv $1 $blobFolder/$1
+
+echo "<figure><img src=\""$(basename $blobFolder)/$1"\" width=\"500px\"><figcaption></figcaption></figure>" | xclip -selection clipboard

nj

@@ -0,0 +1,41 @@
+#!/bin/bash
+defTitle=journal
+defDir=notes
+defTemplate=$HOME/bin/nj-note.md
+defApp=nano #nano,vim,gvim,emacs,atom,subl
+
+title=$1
+basedir=$2
+mdtemplate=$3
+app=$EDITOR
+
+if [[ -z $title ]]; then
+	title=$defTitle
+fi
+
+if [[ -z $basedir ]]; then
+	basedir=$HOME/$defDir
+fi
+
+if [[ -z $mdtemplate ]]; then
+	mdtemplate=$defTemplate
+fi
+
+if [[ -z $app ]]; then
+	app=$defApp
+fi
+
+#basedir=if [[ -z $var 2:-$HOME/$defDir}
+
+fn=$basedir/$(date +"%Y-%m-%d")-$title.md
+
+if [[ -e $fn ]]
+then
+	echo "opening $fn"
+	$app $fn
+else
+	echo "creating $fn"
+	cat $mdtemplate | sed -E "s|(date: ).+|\1$(date --iso-8601='seconds')  |" >> $fn
+	$app $fn
+fi
+

nj-note.md

@@ -0,0 +1,8 @@
+---
+author: James B. Ackman  
+date: 2018-10-26T07:17:26-07:00  
+tags: journal, home  
+layout: post  
+categories: pri  
+---
+

pubmed2bibtex.xsl

@@ -0,0 +1,135 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsl:stylesheet version = "1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+
+<!--
+  - This Extensible Stylesheet Language Transformation file translates XML files
+  - as provided by PubMed into BibTeX files.
+  -
+  - This file was written by Thomas Fischer <fischer@unix-ag.uni-kl.de>
+  - It is released under the GNU Public License version 2 or later.
+  -
+  - To run test this transformation file, run e.g.
+  - wget 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=21351276&retmode=xml' -O - | xsltproc  pubmed2bibtex.xsl -
+  -->
+
+<!-- stylesheet updated by James Ackman <james.ackman@gmail.com> 2018-11-05T22:49:52-08:00 -->
+
+<xsl:output method="text" omit-xml-declaration="yes" indent="no" encoding="UTF-8"/>
+<xsl:strip-space elements="*"/>
+
+<xsl:variable name="smallcase" select="'abcdefghijklmnopqrstuvwxyz'" />
+<xsl:variable name="uppercase" select="'ABCDEFGHIJKLMNOPQRSTUVWXYZ'" />
+
+
+<!-- START HERE -->
+<xsl:template match="/">
+<!-- process each entry -->
+<xsl:apply-templates select="PubmedArticleSet/PubmedArticle"/>
+</xsl:template>
+
+<xsl:template match="PubmedArticle">
+<!-- assuming that there are only journal references -->
+<xsl:text>@article{</xsl:text>
+<xsl:value-of select="MedlineCitation/Article/AuthorList/Author/LastName"/>
+<xsl:value-of select="MedlineCitation/Article/Journal/JournalIssue/PubDate/Year"/>
+<!-- <xsl:text>_</xsl:text><xsl:value-of select="MedlineCitation/PMID" /> -->
+<xsl:apply-templates select="MedlineCitation/Article"/>
+<xsl:apply-templates select="MedlineCitation/KeywordList"/>
+<!-- <xsl:apply-templates select="MedlineCitation/MeshHeadingList"/> -->
+<xsl:apply-templates select="PubmedData/ArticleIdList/ArticleId"/>
+<xsl:text>,
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/</xsl:text><xsl:value-of select="MedlineCitation/PMID"/><xsl:text>},
+  file = {}</xsl:text>
+<xsl:if test="string-length(MedlineCitation/MedlineJournalInfo/NlmUniqueID) > 0"><xsl:text>,
+  nlmuniqueid = {</xsl:text><xsl:value-of select="MedlineCitation/MedlineJournalInfo/NlmUniqueID" /><xsl:text>}</xsl:text></xsl:if>
+<xsl:text>
+}
+
+</xsl:text>
+</xsl:template>
+
+
+<xsl:template match="ArticleId">
+<xsl:choose>
+<xsl:when test="@IdType='doi'">
+<xsl:text>,
+  doi = {</xsl:text><xsl:value-of select="." /><xsl:text>}</xsl:text>
+</xsl:when>
+<xsl:otherwise>
+<xsl:text>,
+  </xsl:text><xsl:value-of select="@IdType" /><xsl:text> = {</xsl:text><xsl:value-of select="." /><xsl:text>}</xsl:text>
+</xsl:otherwise>
+</xsl:choose>
+</xsl:template>
+
+
+<xsl:template match="Article">
+<xsl:text>,
+  title = {</xsl:text><xsl:value-of select="ArticleTitle" /><xsl:text>}</xsl:text>
+<xsl:apply-templates select="AuthorList" />
+<xsl:apply-templates select="Journal" />
+<xsl:text>,
+  pages = {</xsl:text><xsl:value-of select="Pagination/MedlinePgn" /><xsl:text>}</xsl:text>
+<xsl:if test="string-length(Abstract/AbstractText) > 0"><xsl:text>,
+  abstract = {</xsl:text><xsl:value-of select="Abstract/AbstractText" /><xsl:text>}</xsl:text></xsl:if>
+</xsl:template>
+
+
+
+<xsl:template match="Journal">
+<!-- going for the journal title's abbreviation with MedlineTA instead of ISOAbbreviation, looks better -->
+<xsl:text>,
+  journal = {</xsl:text><xsl:value-of select="/PubmedArticleSet/PubmedArticle/MedlineCitation/MedlineJournalInfo/MedlineTA" /><xsl:text>}</xsl:text>
+<xsl:if test="string-length(JournalIssue/ISSN) > 0"><xsl:text>,
+  issn = {</xsl:text><xsl:value-of select="ISSN" /><xsl:text>}</xsl:text></xsl:if>
+<xsl:if test="string-length(JournalIssue/Volume) > 0"><xsl:text>,
+  volume = {</xsl:text><xsl:value-of select="JournalIssue/Volume" /><xsl:text>}</xsl:text></xsl:if>
+<xsl:if test="string-length(JournalIssue/Issue) > 0"><xsl:text>,
+  number = {</xsl:text><xsl:value-of select="JournalIssue/Issue" /><xsl:text>}</xsl:text></xsl:if>
+<xsl:if test="string-length(JournalIssue/PubDate/Year) > 0"><xsl:text>,
+  year = {</xsl:text><xsl:value-of select="JournalIssue/PubDate/Year" /><xsl:text>}</xsl:text></xsl:if>
+<xsl:if test="string-length(JournalIssue/PubDate/Month) > 0"><xsl:text>,
+  month = {</xsl:text><xsl:value-of select="JournalIssue/PubDate/Month" /><xsl:text>}</xsl:text></xsl:if>
+<!--  month = {</xsl:text><xsl:value-of select="translate(JournalIssue/PubDate/Month, $uppercase, $smallcase)" /><xsl:text>}</xsl:text></xsl:if> -->
+</xsl:template>
+
+
+<xsl:template match="AuthorList">
+<xsl:text>,
+  author = {</xsl:text>
+<xsl:apply-templates select="Author"/>
+<xsl:if test="@CompleteYN = 'N'"><xsl:text> and others</xsl:text></xsl:if>
+<xsl:text>}</xsl:text>
+</xsl:template>
+
+<xsl:template match="Author">
+<xsl:if test="position() > 1"><xsl:text> and </xsl:text></xsl:if>
+<xsl:apply-templates select="LastName"/><xsl:text>, </xsl:text>
+<xsl:apply-templates select="ForeName"/>
+</xsl:template>
+
+
+<xsl:template match="KeywordList">
+<xsl:text>,
+  keywords = {</xsl:text>
+<xsl:for-each select="Keyword">
+<xsl:value-of select="."/><xsl:text>; </xsl:text>
+</xsl:for-each>
+<xsl:for-each select="/PubmedArticleSet/PubmedArticle/MedlineCitation/MeshHeadingList/MeshHeading">
+<xsl:value-of select="DescriptorName"/><xsl:text>; </xsl:text>
+</xsl:for-each>
+<xsl:text>}</xsl:text>
+</xsl:template>
+
+<!--
+<xsl:template match="MeshHeadingList">
+<xsl:text>,
+  mesh = {</xsl:text>
+<xsl:for-each select="MeshHeading">
+<xsl:value-of select="DescriptorName"/><xsl:text>; </xsl:text>
+</xsl:for-each>
+<xsl:text>}</xsl:text>
+</xsl:template>
+-->
+
+</xsl:stylesheet>

reveal.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#installation: place in home directory and make this file executable `chmod u=rwX,go= reveal.sh`
+#usage example: `./reveal.sh neuroanatomy1.md`
+
+appPath="$HOME/projects/dev/reveal.js"
+
+if [[ ! -d $appPath ]]; then
+    echo "reveal.js not found"
+    exit 1
+else
+    cd $appPath
+fi
+
+fn=$1 #markdown document to render e.g. neuroanatomy1.md
+if [[ ! -e $fn ]]; then
+    ln -s $fn $(basename $fn)
+fi
+
+#add markdown filename to reveal placeholder start file
+sed -i -E "s|(<section data-markdown=\")[A-Za-z0-9\.-]*(\" )|\1$fn\2|" index.html
+npm start
+

sdoi.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+#sdoi - search for doi and append bibtex entry to db
+# usage:
+#  sdoi.sh 'doi.string'
+
+#Setup defaults
+styleSheet="$HOME/bin/pubmed2bibtex.xsl"
+bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
+pdfPathOut="$HOME/projects/bibd/papers"
+relPath=$(basename $pdfPathOut)
+doi=$1
+fn=$2
+
+set -e #exit if an error
+
+uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$doi&field=doi&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s#<Id>([0-9]+)</Id>#\1#")
+
+if [ -z "$uid" ]; then
+  echo "pubmed id not found"
+  exit 1
+fi
+
+#request pubmed xml and transform into bibtex
+curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$uid&retmode=xml" > $uid.xml
+xsltproc --novalid $styleSheet $uid.xml > $uid.bib
+
+#decide whether to process and move an associated pdf or just exit
+if [ -z "$fn" ]; then
+
+  if [[ -z $(rg $uid $bibdFileOut) ]]; then
+    #import bibtex
+    echo "importing $uid.bib"
+    cat $uid.bib >> $bibdFileOut
+  else
+    echo "$uid already found in $bibdFileOut, exiting"
+  fi
+  #clean up
+  rm $uid.xml $uid.bib
+  exit 1
+
+else
+  #extract some strings to make a nice filename for the pdf
+  key="LastName"; 
+  author=$(grep $key --max-count=1 $uid.xml | sed -E "s#\W*<$key>(.+)</$key>\W*#\1#")
+
+  key="MedlineTA"; 
+  journal=$(grep $key --max-count=1 $uid.xml | sed -E "s#\W*<$key>(.+)</$key>\W*#\1#" | tr -d " ")
+
+  key1="PubDate"; 
+  key2="Year"; year=$(awk "/<$key1>/,/<\/$key1>/" $uid.xml | grep $key2 | sed -E "s#\W*<$key2>(.+)</$key2>\W*#\1#")
+
+  fn2=${author}_${journal}$year-$uid.pdf
+
+  #move pdf file to papers repository, add file name to bibtex file field
+  mv $fn $pdfPathOut/$fn2
+  echo "moved to $pdfPathOut/$fn2"
+  sed -i -E "s|(\W*file = \{).*(\}.*)|\1$relPath/$fn2\2|" $uid.bib
+
+  if [[ -z $(rg $uid $bibdFileOut) ]]; then
+    #import bibtex
+    echo "importing $uid.bib"
+    cat $uid.bib >> $bibdFileOut
+  else
+    echo "$uid already found in $bibdFileOut, exiting"
+  fi
+
+  #clean up
+  rm $uid.xml $uid.bib
+fi

shrinkpdf.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+#shrinkpdf - resize pdf to smaller size. Warning: if no second file name is provided, the default behavior is to overwrite the original pdf
+# usage:
+#  shrinkpdf.sh large.pdf
+#  shrinkpdf.sh large.pdf small.pdf
+# dependencies:
+#  ps2pdf from Ghostscript
+#  mktemp from GNU Coreutils
+
+#Setup defaults
+fn=$1
+fn2=$2
+set -e #exit if an error
+
+#decide whether to use a provided new file name or too write over the original filename
+if [ -z "$fn2" ]; then
+  #clean up
+  tmpName=$(mktemp $fn.XXXXXXX)
+  ps2pdf $fn $tmpName
+  #echo $tmpName
+  rm $fn
+  mv $tmpName $fn
+  chmod u=rw,go=r $fn
+else
+  ps2pdf $fn $fn2
+fi

spmid.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+#spmid - search for pubmed id and append bibtex entry to db
+# usage:
+#  spmid.sh '12345678'
+#  spmid.sh '12345678' download.pdf
+
+#Setup defaults
+styleSheet="$HOME/bin/pubmed2bibtex.xsl"
+bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
+pdfPathOut="$HOME/projects/bibd/papers"
+relPath=$(basename $pdfPathOut)
+uid=$1
+fn=$2
+
+set -e #exit if an error
+
+#request pubmed xml and transform into bibtex
+curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$uid&retmode=xml" > $uid.xml
+xsltproc --novalid $styleSheet $uid.xml > $uid.bib
+
+#decide whether to process and move an associated pdf or just exit
+if [ -z "$fn" ]; then
+  #clean up
+  rm $uid.xml $uid.bib
+  exit 1
+else
+  #extract some strings to make a nice filename for the pdf
+  key="LastName"; 
+  author=$(grep $key --max-count=1 $uid.xml | sed -E "s#\W*<$key>(.+)</$key>\W*#\1#")
+
+  key="MedlineTA"; 
+  journal=$(grep $key --max-count=1 $uid.xml | sed -E "s#\W*<$key>(.+)</$key>\W*#\1#" | tr -d " ")
+
+  key1="PubDate"; 
+  key2="Year"; year=$(awk "/<$key1>/,/<\/$key1>/" $uid.xml | grep $key2 | sed -E "s#\W*<$key2>(.+)</$key2>\W*#\1#")
+
+  fn2=${author}_${journal}$year-$uid.pdf
+
+  #move pdf file to papers repository, add file name to bibtex file field
+  mv $fn $pdfPathOut/$fn2
+  echo "moved to $pdfPathOut/$fn2"
+  sed -i -E "s|(\W*file = \{).*(\}.*)|\1$relPath/$fn2\2|" $uid.bib
+
+  if [[ -z $(rg $uid $bibdFileOut) ]]; then
+    #import bibtex
+    echo "importing $uid.bib"
+    cat $uid.bib >> $bibdFileOut
+  else
+    echo "$uid already found in $bibdFileOut, exiting"
+  fi
+  
+  #clean up
+  rm $uid.xml $uid.bib
+fi

spubmed.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+#spubmed.sh - search for pubmed for author, journal, year
+# usage:
+#  spubmed.sh 'kaas' 'trends+neurosci' '1995'
+#  spubmed.sh 'rakic' 'j+comp+neurol' '1972'
+
+#Setup defaults
+styleSheet="$HOME/bin/pubmed2bibtex.xsl"
+bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
+pdfPathOut="$HOME/projects/bibd/papers"
+relPath=$(basename $pdfPathOut)
+author=$1
+journal=$2
+year=$3
+
+set -e #exit if an error
+
+uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$author[au]+AND+$journal[ta]+AND+$year[dp]&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s#<Id>([0-9]+)</Id>#\1#")
+
+if [ -z "$uid" ]; then
+  echo "pubmed id not found"
+  exit 1
+fi
+
+if [[ $(echo $uid | wc -w) -gt 1 ]]; then
+  echo 'more than one pmid found, going to pubmed'
+  exturl="https://www.ncbi.nlm.nih.gov/pubmed/?term=$author[au]+AND+$journal[ta]+AND+$year[dp]"
+  xdg-open $exturl
+  exit 1
+fi
+
+echo $uid | xclip -selection clipboard
+echo $uid
+
+# #request pubmed xml and transform into bibtex
+# curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$uid&retmode=xml" > $uid.xml
+# xsltproc --novalid $styleSheet $uid.xml > $uid.bib
+# 
+# #import bibtex
+# echo "importing $uid.bib"
+# cat $uid.bib >> $bibdFileOut
+# 
+# #clean up
+# rm $uid.xml $uid.bib

woola

@@ -0,0 +1,22 @@
+#!/bin/bash
+#helper startup script for woola
+appPath="$HOME/projects/dev/woola"
+configFile=$HOME/.config/woola/config.js
+
+if [[ -e $configFile ]] && [[ ! -e config.js ]]; then
+    ln -s $configFile config.js
+fi
+
+if [[ ! -d css ]]; then
+    ln -s $HOME/projects/dev/libcss css
+fi
+
+#if [[ ! -d js ]]; then
+#    ln -s $appPath/js js
+#fi
+
+#if [[ ! -d figures ]]; then
+#    ln -s $HOME/figures figures
+#fi
+node $appPath/lib/index.js
+

ws1

@@ -0,0 +1,7 @@
+#!/bin/bash
+#urxvt -e "dimr &"
+urxvt -cd $HOME/projects &
+urxvt &
+urxvt &
+urxvt -cd $HOME/notes &
+