[med-svn] [SCM] aghermann branch, master, updated. 5727b0b7844548ed4c4fceab25995fc02b87da50

[Andrei Zavada]

The following commit has been merged in the master branch:
commit cd1c0da9c3b9fcd6da8bbed0bfc97647b5cc5329
Author: Andrei Zavada <johnhommer at gmail.com>
Date:   Tue Dec 4 02:16:19 2012 +0200

    update doc/org

diff --git a/doc/org/Makefile.am b/doc/org/Makefile.am
index 5a366af..a0e7792 100644
--- a/doc/org/Makefile.am
+++ b/doc/org/Makefile.am
@@ -1,15 +1,17 @@
 EXTRA_DIST = \
 	aghermann.org.in \
-	mc.org \
+	usage.org \
 	model.org \
-	usage.org
+	mc.org \
+	swu.org
 
 if DO_EMACS_ORGMODE_CONV
 genhtml_DATA = \
 	aghermann.html \
-	mc.html \
+	usage.html \
 	model.html \
-	usage.html
+	mc.html \
+	swu.html
 
 %.html: %.org
 	$(ORGMODE_EMACS) --batch -Q -l org $< -f org-export-as-html
diff --git a/doc/org/aghermann.org.in b/doc/org/aghermann.org.in
index 82c658b..b2eb2ee 100644
--- a/doc/org/aghermann.org.in
+++ b/doc/org/aghermann.org.in
@@ -25,9 +25,8 @@ long sleepers, early /vs/ late, etc.
   want to eke out the extra couple of percent in speed -O3 will
   probably yield (or if your distro is of non-Debian lineage).
 
-  The project’s public Git repositories are hosted on [[https://github.com/hmmr/aghermann][GitHub]] and,
-  historically, also at [[http://sourceforge.net/projects/aghermann][SourceForge]].
-
+  The project’s public Git repositories are hosted on [[https://github.com/hmmr/aghermann][GitHub]], on
+  [[http://anonscm.debian.org/gitweb/?p=debian-med/aghermann.git][Debian servers]] and, historically, also at [[http://sourceforge.net/projects/aghermann][SourceForge]].
 
 * Features
 ** Sleep experiment recording manager
@@ -111,9 +110,9 @@ long sleepers, early /vs/ late, etc.
       0.25, 0.5 and 1 Hz and combined into larger frequency ranges, or
       conventional bands (delta, gamma etc).
 
-    + *Slow Wave Upswing* (SWU), an experimental metric representing
+    + *Slow Wave Upswing* ([[file:swu.org][SWU]]), an experimental metric representing
       a measure of uniformity/simultaneity of neurons generating a
-      slow wave front.
+      slow wave.
 
     + [[http://www.ncbi.nlm.nih.gov/pubmed/11008419][*EEG Microcontinuity*]] [[file:mc.org]["lite"]].
 
@@ -135,7 +134,6 @@ long sleepers, early /vs/ late, etc.
 
    + All graphic presentations can be saved in SVG format.
 
-
 * Accessory utilities to handle EDF files
 Included as separate programs are companion utilities to view/modify
 EDF header and create EDF files from plain ASCII tsv files.
@@ -151,7 +149,6 @@ EDF header and create EDF files from plain ASCII tsv files.
    drop channels from an edf file.  Refer to its man page for
    details.  More operations are planned.
 
-
 * Notes on security and accessibility
 
    + There is no consideration specially given to potential security
@@ -178,7 +175,6 @@ EDF header and create EDF files from plain ASCII tsv files.
      on the item or pressing Enter.  This saved me a few dialog boxes
      along the way.)
 
-
 * Feedback/bugreports
 
   Should you find Aghermann useful (in its scoring capacity only, or
diff --git a/doc/org/swu.org b/doc/org/swu.org
new file mode 100644
index 0000000..f9b9157
--- /dev/null
+++ b/doc/org/swu.org
@@ -0,0 +1,20 @@
+#+TITLE: EEG Slow Wave Upswing
+#+AUTHOR:    Andrei Zavada
+#+EMAIL:     johnhommer at gmail.com
+#+LANGUAGE:  en
+#+OPTIONS: toc:nil num:nil LaTeX:t
+#+LINK_UP:   
+#+LINK_HOME: aghermann.html
+
+* Slow Wave Upswing
+  Introduced in version 0.7.5, *SWU* is a poor man's take on measuring
+  the local synchronicity of neurons acting together to produce a slow
+  wave.
+
+  It is computed as a total sum, over a page, of area under the curve
+  of the signal's first derivative where it is positive, discarding
+  periods shorter than a certain threshold.
+
+  SWU should to be lower where slow waves have front interrupted by a
+  `kink'. It may be extended to also degrade in presence of a slow
+  wave terminating in a peak with many (rather than few) local minima.
diff --git a/doc/org/usage.org b/doc/org/usage.org
index 21125d7..422bbf5 100644
--- a/doc/org/usage.org
+++ b/doc/org/usage.org
@@ -29,7 +29,6 @@
 
    If any edf file needs fixing its header, use edfhed or edfhed-gtk.
 
-
 * Notes on Signal Type and Label fields in EDF headers
 
    Make sure the =Label= field is (without quotes) either of
@@ -57,7 +56,6 @@
    At present, EDF+ features (in particular, discontinuous signals
    and sub-fields of the `PatientID' field) are not supported.
 
-
 * Measurements Overview
 
   All properly placed recordings will appear on the =1. Measurements=
@@ -149,7 +147,6 @@
    save them as a named profile, and subsequently apply AD globally
    to all your recordings.
 
-
 * Refining EEG further with ICA
 
   You can also try to isolate/distill EEG signals with *Independent
@@ -164,7 +161,6 @@
 
   + *Punch* out some ICs and remix.
 
-
 * EEG score import/export
 
   The import filter reads the tokens and attempt to identify the
@@ -186,7 +182,6 @@
   applied instead.  Do some sed work to change the score codes
   accordingly.
 
-
 * Preparing the profiles for simulations
 
   Once you are done preparing your SWA profiles, proceed
@@ -205,7 +200,6 @@
 
   Likewise, AZ1 amendment is ineffective for single-episode profiles.
 
-
 * Running the simulations
 
   Then, double-click on a row in the =2. Simultions= tab.  If all

-- 
Sleep experiment manager