[med-svn] [aghermann] 02/34: update doc/aghermann.org

[andrei zavada]

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hmmr-guest pushed a commit to branch master
in repository aghermann.

commit 612bf10c354921208b2e9b21d70e8712b3f60a56
Author: Andrei Zavada <hmmr at ra>
Date:   Sun Nov 10 16:10:18 2013 +0200

    update doc/aghermann.org
---
 upstream/doc/org/aghermann.org.in | 73 +++++++++++++++++++++++++++++----------
 upstream/doc/org/basic_score.lua  |  1 +
 2 files changed, 55 insertions(+), 19 deletions(-)

diff --git a/upstream/doc/org/aghermann.org.in b/upstream/doc/org/aghermann.org.in
index 37e35f1..7c38074 100644
--- a/upstream/doc/org/aghermann.org.in
+++ b/upstream/doc/org/aghermann.org.in
@@ -38,21 +38,6 @@ long sleepers, early /vs/ late, etc.
 
 | Aghermann provides a capable facility for displaying EEG and accompanying recordings, such as EOG and EMG, saved in plain EDF or EDF+C (European Data Format) files. | [[file:img/sf.png][img/sf-t.png]]   |
 
-*** No (serious) scoring asistance
-
-   It has been considered, and even planned, but never matured enough
-   to overcome the distrust of at least one well-to-do sleep
-   researcher.
-
-   There is a very basic scoring assistant though, which will mark a
-   page as NREM3 if the ratio of power in the 2-3 Hz range in that
-   page is greater than 1.5 times power in 5-8 Hz range.  After
-   consultations with certain knowledgeable figures in sleep research,
-   however, I remain ever firmly convinced that, the five lines of
-   code it consists of, are already five lines too many.
-
-   Scores can be imported from plain ASCII files, and exported.
-
 *** Artifact detection
 
    *Artifact detection* comes as a side-effect in the computation of [[http://www.ncbi.nlm.nih.gov/pubmed/11008419][EEG
@@ -107,7 +92,14 @@ long sleepers, early /vs/ late, etc.
     determined as a shift of one signal's band-passed component against
     another such that the difference between them is minimal.
 
-*** Scoring
+*** Automatic scoring
+
+   It has been considered but never matured enough to overcome the
+   distrust of at least one well-to-do sleep researcher.  The bright
+   solution I found is, however, to delegate it to the user, one
+   much desirable side effect of this being, I will not be blamed, let
+   alone laughed at, for my scoring algorithm performing like speech
+   recognition in Windows 95.
 
 **** Manual scoring
      Recordings can be conveniently scored manually; scores can be imported/exported in plain ASCII.
@@ -115,9 +107,52 @@ long sleepers, early /vs/ late, etc.
 **** Automated scoring
      Scoring can also be scripted, in Lua.
 
-     To enable this scripted scoring, you have access, from within
-     Lua, to the three sleep profiles for individual EEG channels in
-     your montage, as well as to 
+     To enable such scripted scoring, you have access, from within
+     Lua, to the following functions (in lua-like pseudocode):
+
+#+BEGIN_SRC lua
+     function get_channel_list ()
+       return n_channels, ch1, ch2, ...
+     end
+
+     function get_channel_list_of_type (type)
+       return n_channels, ch1, ch2, ...
+     end
+
+     function get_channel_data (channel)
+       return n_full_pages, n_total_pages, pagesize, samplerate
+     end
+
+     function get_psd (channel, start_page, end_page_inclusive, freq_min, freq_max)
+       return vector_of_psd_values_in_given_range
+     end
+
+     function get_mc (channel, start_page, end_page_inclusive, freq0, unused)
+       return vector_of_mc_values_at_given_freq
+     end
+
+     function get_swu (channel, start_page, end_page_inclusive, freq0, unused)
+       return vector_of_swu_values_at_given_freq
+     end
+
+     function get_signal_envelope (channel, page, scope, dt)
+       return vector_of_signal_envelope_breadth_values_taken_at_dt_intervals
+     end
+
+     function get_page_dirty (channel, page)
+       return portion_0thru1_of_signal_marked_as_artifact
+     end
+#+END_SRC
+
+     And, to score a page, use score (page, score).
+
+     The above functions are defined in [[basic_score.lua]], which
+     appears as a default, system scoring profile.  This script is
+     barely useful in this form (it only takes into accout the first
+     EEG channel, and only tries to detect NREM).  You are encouraged
+     to duplicate the relevant boilerplate from it to create a more
+     advanced scoring script.
+
 
 ** SWA profiles
 
diff --git a/upstream/doc/org/basic_score.lua b/upstream/doc/org/basic_score.lua
new file mode 120000
index 0000000..fa109fc
--- /dev/null
+++ b/upstream/doc/org/basic_score.lua
@@ -0,0 +1 @@
+/home/hmmr/P/C/Aghermann/upstream/data/basic_score.lua
\ No newline at end of file

-- 
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