[med-svn] r13446 - in trunk/packages/ecell/trunk/debian: . source
Author: alteholz
Date: 2013-04-30 20:28:23 + (Tue, 30 Apr 2013)
New Revision: 13446
Added:
trunk/packages/ecell/trunk/debian/source/
trunk/packages/ecell/trunk/debian/source/format
Modified:
trunk/packages/ecell/trunk/debian/changelog
trunk/packages/ecell/trunk/debian/compat
trunk/packages/ecell/trunk/debian/control
trunk/packages/ecell/trunk/debian/rules
Log:
some progress until boost errors occured
Modified: trunk/packages/ecell/trunk/debian/changelog
===
--- trunk/packages/ecell/trunk/debian/changelog 2013-04-29 21:04:06 UTC (rev
13445)
+++ trunk/packages/ecell/trunk/debian/changelog 2013-04-30 20:28:23 UTC (rev
13446)
@@ -4,6 +4,7 @@
* TODO: check dependencies:
- is it correct to replace python2.2-xmlbase by python?
- is it correct to replace python2.2-numeric by python-numpy?
+ * TODO: take care of boost compile errors
[ Thorsten Alteholz ]
* new upstream version
Modified: trunk/packages/ecell/trunk/debian/compat
===
--- trunk/packages/ecell/trunk/debian/compat2013-04-29 21:04:06 UTC (rev
13445)
+++ trunk/packages/ecell/trunk/debian/compat2013-04-30 20:28:23 UTC (rev
13446)
@@ -1 +1 @@
-4
+9
Modified: trunk/packages/ecell/trunk/debian/control
===
--- trunk/packages/ecell/trunk/debian/control 2013-04-29 21:04:06 UTC (rev
13445)
+++ trunk/packages/ecell/trunk/debian/control 2013-04-30 20:28:23 UTC (rev
13446)
@@ -4,13 +4,35 @@
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller moel...@pzr.uni-rostock.de
-Build-Depends: debhelper (= 4.0.0), python-numpy, python-dev, python-gtk2,
python-glade2, g++ (= 3.3), libgsl0-dev, libboost-python-dev, automake,
autoconf, libtool, python-gnome2, expect, doxygen, graphviz, docbook-utils,
ghostscript, docbook-to-man
+Build-Depends: debhelper (= 9),
+ python-numpy,
+ python-dev,
+ python-gtk2,
+ python-glade2,
+ g++ (= 3.3),
+ libgsl0-dev,
+ libboost-python-dev,
+ automake,
+ autoconf,
+ libtool,
+ python-gnome2,
+ python-ply,
+ expect,
+ doxygen,
+ graphviz,
+ docbook-utils,
+ ghostscript,
+ docbook-to-man
Standards-Version: 3.6.0
Homepage: http://www.e-cell.org/
Package: ecell
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, libgsl0, libgnome2-0,
python-numpy, python-glade2
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libgsl0,
+ libgnome2-0,
+ python-numpy,
+ python-glade2
Description: Concept and environment for constructing virtual cells on
computers
The E-Cell Project is an international research project aiming at
developing necessary theoretical supports, technologies and software
Modified: trunk/packages/ecell/trunk/debian/rules
===
--- trunk/packages/ecell/trunk/debian/rules 2013-04-29 21:04:06 UTC (rev
13445)
+++ trunk/packages/ecell/trunk/debian/rules 2013-04-30 20:28:23 UTC (rev
13446)
@@ -9,17 +9,10 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-# This has to be exported to make some magic below work.
-export DH_OPTIONS
-
-# These are used for cross-compiling and for saving the configure script
-# from having to guess our platform (since we know it already)
DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
-
-CFLAGS = -Wall -g
-
+CFLAGS += -Wall -g
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
CFLAGS += -O0
else
@@ -29,126 +22,168 @@
INSTALL_PROGRAM += -s
endif
-configure: configure.in
- dh_testdir
+
+%:
+ dh $@
+
+override_dh_auto_configure:
./autogen.sh --enable-static=no --host=$(DEB_HOST_GNU_TYPE)
--build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man
--infodir=\$${prefix}/share/info
-
-config.status: configure
- dh_testdir
- # Add here commands to configure the package.
CFLAGS=$(CFLAGS) ./configure --enable-static=no
--host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr
--mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info
#CFLAGS=$(CFLAGS) ./configure --disable-gtk
--host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr
--mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info
-#Architecture
-build: ecell.1 build-arch build-indep
-
-build-arch: build-arch-stamp
-build-arch-stamp: config.status
-
- # Add here commands to compile the arch part of the package.
- $(MAKE)
- touch build-arch-stamp
-
-build-indep: build-indep-stamp
-build-indep-stamp: config.status
-
- # Add here commands to compile the indep part of the package.
+override_dh_auto_build:
$(MAKE) doc
- touch
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit afd290475deb1fe41eb07092034d7bf735fc2535
Author: Andrei Zavada johnhom...@gmail.com
Date: Mon Apr 22 18:17:59 2013 +0300
in-/decrement scale individually with Ctrl, all msmts at once with
Ctrl+Shift
diff --git a/src/ui/mw/measurements.cc b/src/ui/mw/measurements.cc
index 64ae161..9a77170 100644
--- a/src/ui/mw/measurements.cc
+++ b/src/ui/mw/measurements.cc
@@ -298,24 +298,27 @@ draw_timeline( cairo_t *cr) const
void
aghui::SExpDesignUI::
-modify_profile_scales( const GdkScrollDirection d)
+modify_active_profile_scale( const GdkScrollDirection d)
{
- switch ( d ) {
- case GDK_SCROLL_DOWN:
- profile_scale_psd /= 1.05;
- profile_scale_swu /= 1.05;
- profile_scale_mc /= 1.05;
- break;
- case GDK_SCROLL_UP:
- profile_scale_psd *= 1.05;
- profile_scale_swu *= 1.05;
- profile_scale_mc *= 1.05;
- break;
- default:
- break;
+ auto fac = (d == GDK_SCROLL_DOWN) ? 1/1.05 : 1.05;
+ switch ( display_profile_type ) {
+ case metrics::TType::psd: profile_scale_psd *= fac; break;
+ case metrics::TType::swu: profile_scale_swu *= fac; break;
+ case metrics::TType::mc : profile_scale_mc *= fac; break;
+ default: break;
}
}
+void
+aghui::SExpDesignUI::
+modify_profile_scales( const GdkScrollDirection d)
+{
+ auto fac = (d == GDK_SCROLL_DOWN) ? 1/1.05 : 1.05;
+ profile_scale_psd *= fac;
+ profile_scale_swu *= fac;
+ profile_scale_mc *= fac;
+}
+
// Local Variables:
// Mode: c++
// indent-tabs-mode: 8
diff --git a/src/ui/mw/measurements_cb.cc b/src/ui/mw/measurements_cb.cc
index ceef0f9..7470f16 100644
--- a/src/ui/mw/measurements_cb.cc
+++ b/src/ui/mw/measurements_cb.cc
@@ -127,10 +127,15 @@ daSubjectTimeline_scroll_event_cb(
auto J = *(SExpDesignUI::SSubjectPresentation*)userdata;
auto ED = J._p._p;
- if ( event-state GDK_CONTROL_MASK ) {
+ if ( event-state (GDK_CONTROL_MASK | GDK_SHIFT_MASK) ) {
ED.modify_profile_scales( event-direction);
gtk_widget_queue_draw( (GtkWidget*)ED.cMeasurements);
return TRUE;
+
+ } else if ( event-state GDK_CONTROL_MASK ) {
+ ED.modify_active_profile_scale( event-direction);
+ gtk_widget_queue_draw( (GtkWidget*)ED.cMeasurements);
+ return TRUE;
} else
return FALSE;
}
diff --git a/src/ui/mw/mw.hh b/src/ui/mw/mw.hh
index 38391b3..3aaa244 100644
--- a/src/ui/mw/mw.hh
+++ b/src/ui/mw/mw.hh
@@ -264,6 +264,7 @@ class SExpDesignUI
profile_scale_swu,
profile_scale_mc;
double calculate_profile_scale();
+ void modify_active_profile_scale( GdkScrollDirection);
void modify_profile_scales( GdkScrollDirection);
boolautoscale;
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit a8b11d915e50f7c1ee1f3cf49e6e4e3f72085a96
Author: Andrei Zavada johnhom...@gmail.com
Date: Thu Apr 25 19:16:55 2013 +0300
elicit embedded annotations on montage
diff --git a/src/ui/sf/montage.cc b/src/ui/sf/montage.cc
index 36c2cd4..71fb38d 100644
--- a/src/ui/sf/montage.cc
+++ b/src/ui/sf/montage.cc
@@ -778,26 +778,27 @@ draw_montage( cairo_t* cr)
autowa = fmod(aa, evpz) / evpz * da_wd,
ww = (ae - aa) / evpz * da_wd;
- if ( A.type == sigfile::SAnnotation::TType::plain ) {
- int disp = 0 +
- ((last_z A.span.a)
-? ++overlap_count * 5
-: (overlap_count = 0));
- last_z = A.span.z;
-
-
_p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr);
-
- cairo_set_line_width( cr, 2.5);
- cairo_rectangle( cr, wa, 0, ww, da_ht);
- cairo_fill( cr);
- cairo_stroke( cr);
+ int disp = 0 +
+ ((last_z A.span.a)
+? ++overlap_count * 5
+: (overlap_count = 0));
+ last_z = A.span.z;
+
+
_p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr, .9);
+ cairo_set_line_width( cr, 2.5);
+ cairo_rectangle( cr, wa, 0, ww, da_ht);
+ cairo_stroke( cr);
- cairo_select_font_face( cr, serif,
CAIRO_FONT_SLANT_ITALIC, CAIRO_FONT_WEIGHT_NORMAL);
- cairo_set_font_size( cr, 11);
- cairo_set_source_rgb( cr, 0., 0., 0.);
- cairo_move_to( cr, fmod(aa, evpz) / evpz *
da_wd, da_ht - 12 - disp);
- cairo_show_text( cr, A.label.c_str());
- }
+
_p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr);
+ cairo_rectangle( cr, wa, 0, ww, da_ht);
+ cairo_fill( cr);
+ cairo_stroke( cr);
+
+ cairo_select_font_face( cr, serif,
CAIRO_FONT_SLANT_ITALIC, CAIRO_FONT_WEIGHT_NORMAL);
+ cairo_set_font_size( cr, 11);
+ cairo_set_source_rgb( cr, 0., 0., 0.);
+ cairo_move_to( cr, fmod(aa, evpz) / evpz * da_wd, da_ht
- 12 - disp);
+ cairo_show_text( cr, A.label.c_str());
}
}
case TMode::showing_remixed:
diff --git a/src/ui/sf/sf.cc b/src/ui/sf/sf.cc
index a74d29c..b669686 100644
--- a/src/ui/sf/sf.cc
+++ b/src/ui/sf/sf.cc
@@ -142,10 +142,12 @@ SScoringFacility (agh::CSubject J,
for ( auto H : channels )
for ( auto A : H.crecording.F().annotations() )
common_annotations.push_back( {H.crecording.F(), A});
// bitch
- sort( common_annotations.begin(), common_annotations.end(),
+ common_annotations.sort(
[]( const pairconst sigfile::CSource*, const
sigfile::SAnnotation* a1,
const pairconst sigfile::CSource*, const
sigfile::SAnnotation* a2)
{ return *a1.second *a2.second; });
+ common_annotations.unique();
+ printf( collected %zu embedded annotations\n,
common_annotations.size());
// count n_eeg_channels
n_eeg_channels =
diff --git a/src/ui/sf/sf.hh b/src/ui/sf/sf.hh
index d334981..ac60163 100644
--- a/src/ui/sf/sf.hh
+++ b/src/ui/sf/sf.hh
@@ -314,7 +314,7 @@ class SScoringFacility
update_all_channels_profile_display_scale();
// collected common annotations
- vectorpairconst sigfile::CSource*, const sigfile::SAnnotation*
+ listpairconst sigfile::CSource*, const sigfile::SAnnotation*
common_annotations;
// timeline
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 36d3a2794bd8f8ab98789af210b47bbbd2368012
Author: Andrei Zavada johnhom...@gmail.com
Date: Mon Apr 29 01:45:31 2013 +0300
prepare for 0.9.0
diff --git a/ChangeLog b/ChangeLog
index fccb970..917fa7c 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -6,12 +6,17 @@ v.0.9 (2013-xx-xx)
* Proper file size checks in CEDFFile ctor.
* Don't read last sidecar annotation twice.
* Support EDF+, including embedded annotations.
+ * edfhed: show embedded annotations with -a.
* Make all timestamps in sidecar files (a) relative to recording
start, (b) expressed in seconds, to be consistent with embedded
annotations.
* Fix a SF crash when getting PSD on montage having channels with
variable sample rate, on OMP-enabled hosts.
* Fix a SF crash with montages with ('z'-'a') channels.
+ * Expose general mouse scroll sensitivity on Setup-General
+ settings tab.
+ * Bind F1..3 to cycle thru profile, session and channel on
+ measurements overview.
v.0.8.2 (2013-04-07)
* Fix GtkScrolledWindow issue in Annotations dialog.
diff --git a/configure.ac b/configure.ac
index baf61b7..d4d5c4d 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,6 +1,6 @@
AC_COPYRIGHT([Copyright (c) 2008-13 Andrei Zavada johnhom...@gmail.com])
-AC_INIT([Aghermann], [0.9.0_rc], [johnhom...@gmail.com])
+AC_INIT([Aghermann], [0.9.0], [johnhom...@gmail.com])
AC_CONFIG_SRCDIR([src/main.cc])
AC_CONFIG_MACRO_DIR([m4])
AC_PREREQ(2.61)
diff --git a/data/mw-dialogs.glade b/data/mw-dialogs.glade
index 8d5fe47..2dbee41 100644
--- a/data/mw-dialogs.glade
+++ b/data/mw-dialogs.glade
@@ -265,7 +265,7 @@
/object
object class=GtkTextBuffer id=tEDFFileDetailsReport/
object class=GtkDialog id=wAbout
-property name=width_request616/property
+property name=width_request716/property
property name=height_request429/property
property name=can_focusFalse/property
property name=border_width10/property
@@ -328,7 +328,7 @@
property name=xalign0/property
property name=xpad5/property
property name=ypad15/property
-property
name=labellt;bgt;lt;biggt;lt;biggt;Aghermann 0.9.0 rc
lt;/biggt;lt;/biggt;lt;/bgt;Jibo
+property
name=labellt;bgt;lt;biggt;lt;biggt;Aghermann 0.9.0
lt;/biggt;lt;/biggt;lt;/bgt;Jibo
lt;a
href=http://johnhommer.com/academic/code/aghermanngt;johnhommer.com/academic/code/aghermannlt;/agt;/property
property name=use_markupTrue/property
/object
@@ -424,7 +424,28 @@ With bug reports, either send yours to lt;a
href=mailto:aghermann-users@lists.
property name=yalign0/property
property name=xpad10/property
property name=ypad10/property
-property name=labellt;biggt;lt;bgt;v.
0.8.2lt;/bgt;lt;/biggt; (2013-04-07)
+property name=labellt;biggt;lt;bgt;v.
0.9.0lt;/bgt;lt;/biggt; (2013-04-27)
+lt;span font=monospacegt;
+ * Parse patient_id field in EDF header and extract subject gender,
+ DOB and id from it.
+ * Remove Subject Info dialog; use edfhed to change EDF header.
+ * Only plot finite profile values on msmt overview.
+ * Proper file size checks in CEDFFile ctor.
+ * Don't read last sidecar annotation twice.
+ * Support EDF+, including embedded annotations.
+ * edfhed: show embedded annotations with -a.
+ * Make all timestamps in sidecar files (a) relative to recording
+ start, (b) expressed in seconds, to be consistent with embedded
+ annotations.
+ * Fix a SF crash when getting PSD on montage having channels with
+ variable sample rate, on OMP-enabled hosts.
+ * Fix a SF crash with montages with (gt;'z'-'a') channels.
+ * Expose general mouse scroll sensitivity on Setup-gt;General
+ settings tab.
+ * Bind F1..3 to cycle thru profile, session and channel on
+ measurements overview.
+lt;/spangt;
+lt;biggt;lt;bgt;v. 0.8.2lt;/bgt;lt;/biggt; (2013-04-07)
lt;span font=monospacegt;
* Fix GtkScrolledWindow issue in Annotations dialog.
* Fix those random omp-related freezes on tree rescan.
@@ -433,13 +454,6 @@ With bug reports, either send yours to lt;a
href=mailto:aghermann-users@lists.
* URL fix for SWU page on jh.com/aghermann.
* Enable subject sort.
lt;/spangt;
-lt;biggt;lt;bgt;v. 0.8.1lt;/bgt;lt;/biggt; (2013-02-24)
-lt;span font=monospacegt;
- * Calculate SWU metric over time.
- * SF: ensure signal line remains visible at high page
- sizes.
- * Fix g++-4.8 build and address some -Wformat warnings.
-lt;/spangt;
(for older entries, see lt;a
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit a4c6bed03348b23d7184bec01cc93111f620e325
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 30 01:57:31 2013 +0300
deal with channels like Fpz-Cz reasonably correctly
diff --git a/src/libsigfile/channel.cc b/src/libsigfile/channel.cc
index 88e960b..fd152a3 100644
--- a/src/libsigfile/channel.cc
+++ b/src/libsigfile/channel.cc
@@ -12,6 +12,8 @@
#include map
#include vector
+#include algorithm
+#include common/string.hh
#include channel.hh
using namespace std;
@@ -108,13 +110,32 @@ template const char*
SChannel::channel_sSChannel::TType::erg( int);
tupleSChannel::TType, int
SChannel::
-figure_type_and_name( const string h)
+figure_type_and_name( const string h_)
{
- for ( auto T : _CT_ )
- for ( size_t i = 0; i T.second.size(); ++i )
- if ( 0 == strcasecmp( h.c_str(), T.second[i]) )
- return make_tuple(T.first, (int)i);
- return make_tuple(SChannel::TType::invalid, -1);
+ auto tt = agh::str::tokens( h_, -);
+ if ( tt.size() == 2 ) {
+ for ( auto T : _CT_ )
+ if ( all_of( tt.begin(), tt.end(),
+[]( const string t)
+{
+return any_of( T.second.begin(),
T.second.end(),
+ []( const string
h)
+ {
+ return 0 ==
strcasecmp( h.c_str(), t.c_str());
+ });
+}) )
+ return make_tuple(T.first, 0); // always
custom, because it's a compound (EEG) channel like Fpz-Oz
+ return make_tuple(TType::other, 0);
+
+ } else if ( tt.size() == 1 ) {
+ for ( auto T : _CT_ )
+ for ( size_t i = 0; i T.second.size(); ++i )
+ if ( strcasecmp( T.second[i], h_.c_str()) == 0
) {
+ return make_tuple(T.first, (int)i);
+ }
+ }
+
+ return make_tuple(TType::other, 0);
}
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 61af3c5bd3e7f647cd8a0fd6a2b4cfe2a0a87fe8
Author: Andrei Zavada johnhom...@gmail.com
Date: Sat Apr 27 13:09:04 2013 +0300
ICM
diff --git a/src/ui/mw/mainmenu_cb.cc b/src/ui/mw/mainmenu_cb.cc
index d6f6432..33ad2ae 100644
--- a/src/ui/mw/mainmenu_cb.cc
+++ b/src/ui/mw/mainmenu_cb.cc
@@ -15,6 +15,7 @@
#include ui/sm/sm.hh
#include ui/sf/sf.hh
+using namespace std;
using namespace aghui;
extern C {
@@ -119,7 +120,7 @@ tvGlobalAnnotations_row_activated_cb(
const gpointer userdata)
{
auto ED = *(SExpDesignUI*)userdata;
- aghui::SExpDesignUI::SAnnotation *ann;
+ SExpDesignUI::SAnnotation *ann;
GtkTreeIter iter;
gtk_tree_model_get_iter( (GtkTreeModel*)ED.mGlobalAnnotations, iter,
path);
gtk_tree_model_get( (GtkTreeModel*)ED.mGlobalAnnotations, iter,
@@ -129,7 +130,7 @@ tvGlobalAnnotations_row_activated_cb(
return;
gtk_widget_hide( (GtkWidget*)ED.wGlobalAnnotations);
- aghui::SScoringFacility* found = nullptr;
+ SScoringFacility* found = nullptr;
for ( auto F : ED.open_scoring_facilities )
if ( F-csubject() == ann-csubject
F-session() == ann-session
@@ -143,7 +144,7 @@ tvGlobalAnnotations_row_activated_cb(
found-set_cur_vpage( pages.a, true);
} else {
ED.using_subject = ED.subject_presentation_by_csubject(
ann-csubject);
- auto SF = new aghui::SScoringFacility( ann-csubject,
ann-session, ann-sepisode.name(), ED);
+ auto SF = new SScoringFacility( ann-csubject, ann-session,
ann-sepisode.name(), ED);
auto pages = ann-page_span( SF-vpagesize());
SF-set_cur_vpage( pages.a, true);
}
@@ -174,7 +175,7 @@ iExpBasicSADetectUltradianCycles_activate_cb(
{
auto ED = *(SExpDesignUI*)userdata;
- aghui::SBusyBlock bb (ED.wMainWindow);
+ SBusyBlock bb (ED.wMainWindow);
using namespace agh;
CExpDesign::TEpisodeFilterFun filter =
@@ -299,9 +300,9 @@ iExpGloballyDetectArtifacts_activate_cb(
throw runtime_error (Fix AD dialog response?);
}
- forward_listaghui::SBusyBlock* bbl;
+ forward_listSBusyBlock* bbl;
for ( auto SFp : ED.open_scoring_facilities )
- bbl.push_front( new aghui::SBusyBlock (SFp-wSF));
+ bbl.push_front( new SBusyBlock (SFp-wSF));
ED.ED - for_all_recordings( op, reporter, filter);
ED.sb_clear();
@@ -343,7 +344,7 @@ iExpGloballySetFilters_activate_cb(
int LPO, HPO, NF;
double LPC, HPC;
- aghui::SUIVarCollection W_V;
+ SUIVarCollection W_V;
W_V.reg( ED.eGlobalFiltersLowPassCutoff, LPC);
W_V.reg( ED.eGlobalFiltersLowPassOrder, LPO);
W_V.reg( ED.eGlobalFiltersHighPassCutoff, HPC);
@@ -352,9 +353,9 @@ iExpGloballySetFilters_activate_cb(
if ( GTK_RESPONSE_OK ==
gtk_dialog_run( ED.wGlobalFilters) ) {
- forward_listaghui::SBusyBlock* bbl;
+ forward_listSBusyBlock* bbl;
for ( auto SFp : ED.open_scoring_facilities )
- bbl.push_front( new aghui::SBusyBlock (SFp-wSF));
+ bbl.push_front( new SBusyBlock (SFp-wSF));
W_V.down();
for ( auto G : ED.ED-groups )
for ( auto J : G.second )
diff --git a/src/ui/mw/measurements_cb.cc b/src/ui/mw/measurements_cb.cc
index fc7be3d..fc780a3 100644
--- a/src/ui/mw/measurements_cb.cc
+++ b/src/ui/mw/measurements_cb.cc
@@ -13,6 +13,7 @@
#include ui/sf/sf.hh
#include mw.hh
+using namespace std;
using namespace aghui;
extern C {
@@ -178,7 +179,7 @@ iSubjectTimelineDetectUltradianCycle_activate_cb(
agh::CSubject::SEpisode *Ep;
if ( ED.using_subject (Ep = ED.using_subject-using_episode) ) {
auto R = Ep-recordings.at(ED.AghH());
- aghui::SBusyBlock bb (ED.wMainWindow);
+ SBusyBlock bb (ED.wMainWindow);
ED.do_detect_ultradian_cycle( R);
}
}
diff --git a/src/ui/mw/mw_cb.cc b/src/ui/mw/mw_cb.cc
index b2964d5..2867678 100644
--- a/src/ui/mw/mw_cb.cc
+++ b/src/ui/mw/mw_cb.cc
@@ -16,6 +16,7 @@
#include mw.hh
#include mw_cb.hh
+using namespace std;
using namespace aghui;
extern C {
@@ -191,13 +192,13 @@ eMsmtProfileType_changed_cb(
params.swa_laden_pages_before_SWA_0 = 0u;
// collect profiles that need to be re-created
- aghui::SBusyBlock *bb = nullptr;
+ SBusyBlock *bb = nullptr;
vectoragh::CProfile* redo_profiles;
for ( auto G : ED.groups )
for ( auto J : G )
if ( J.cprofile and J.cprofile-need_compute( params) )
{
if ( !bb )
- bb = new aghui::SBusyBlock
(ED.wMainWindow);
+
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 705681c5f7d21fa7967d491968ca75c8a1fd5fa0
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 30 01:58:54 2013 +0300
SChannel::figure_type_and_name() does not return TType::invalid
diff --git a/src/libsigfile/channel.hh b/src/libsigfile/channel.hh
index d8f8482..0f61cd0 100644
--- a/src/libsigfile/channel.hh
+++ b/src/libsigfile/channel.hh
@@ -120,11 +120,8 @@ struct SChannel {
SChannel (const string h)
{
tie(_type, _idx) = figure_type_and_name(h);
- if ( _type == TType::invalid ) {
- _type = TType::other;
- _idx = 0; // custom
+ if ( _idx == 0 )
_custom_name = h;
- }
}
SChannel (TType type_, int idx_)
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 28c0f740e2ba12ba849324c827a60d7a9fb82299
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 30 14:35:07 2013 +0300
fix stupid side-effect of one tiny innocent ICM (fb1da0b433)
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index 9d063d2..2edd205 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -783,7 +783,7 @@ _parse_header()
// calculate gain
for ( auto H : channels )
- if ( H.ucd.type() ==
sigfile::SChannel::TType::embedded_annotation ) {
+ if ( H.ucd.type() !=
sigfile::SChannel::TType::embedded_annotation ) {
if ( H.physical_max = H.physical_min ||
H.digital_max = H.digital_min ) {
_status |= nogain;
--
Sleep experiment manager
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit b9a4e3783ee98a83bcb5c5fedd2c9d2af95ef91f Author: Andrei Zavada johnhom...@gmail.com Date: Mon Apr 29 19:16:07 2013 +0300 update man and docs diff --git a/doc/org/aghermann.org.in b/doc/org/aghermann.org.in index 7a66bd2..3cf9ed9 100644 --- a/doc/org/aghermann.org.in +++ b/doc/org/aghermann.org.in @@ -31,12 +31,12 @@ long sleepers, early /vs/ late, etc. * Features ** Sleep experiment recording manager -| Aghermann keeps the recordings in an organized fashion in a tree following an experimental design commonly used in sleep research i.e. groups of subjects sleeping several (timed) episoded per session with recordings from a number of channels. | [[file:img/measurements.png][img/measurements-t.png]] | -| Per-channel annotations, with an experiment-wide dialog for quickly jumping to so bookmarked episodes. | [[file:img/annotations.png][img/annotations-t.png]] | +| Aghermann keeps the recordings in an organized fashion in a tree following an experimental design commonly used in sleep research, /i.e./ groups of subjects sleeping several (timed) episoded per session with recordings from a number of channels. | [[file:img/measurements.png][img/measurements-t.png]] | +| *Per-channel annotations*, as well as annotations *embedded in EDF+* files, with an experiment-wide dialog for quickly jumping to so bookmarked episodes. | [[file:img/annotations.png][img/annotations-t.png]] | ** EDF signal viewing and scoring facility -| Aghermann provides a capable facility for displaying EEG and accompanying recordings, such as EOG and EMG, saved in EDF (European Data Format) files. These recordings can then be conveniently scored; scores can be imported/exported in plain ASCII. | [[file:img/sf.png][img/sf-t.png]] | +| 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 @@ -58,22 +58,22 @@ long sleepers, early /vs/ late, etc. *Artifact detection* comes as a side-effect in the computation of [[http://www.ncbi.nlm.nih.gov/pubmed/11008419][EEG Microcontinuity]], and may or may not meet your expectations. Most parameters affecting artifact detection are exposed for your - tuning. Run with default settings, it tends to be a little too + tuning. Run with default settings, it tends to be a little too eager at the task, though. You can detect *flat signal* portions, too. -*** Filters - - Butterworth Low-pass, high-pass and band-pass filters are - available as well as band-stop (notch) filters at 50 and 60 Hz. - *** Manual artifact marking EEG signals can be manually filtered for artifacts. The PSD analysis is then performed on cleaner pages, greatly enhancing the resulting spectral power profile. +*** Filters + + Butterworth Low-pass, high-pass and band-pass filters are + available as well as band-stop (notch) filters at 50 and 60 Hz. + *** Independent Component Analysis | Independent Component Analysis using [[http://www.cs.helsinki.fi/u/ahyvarin/whatisica.shtml][FastICA]] routines from [[http://itpp.sourceforge.net/current/group__fastica.html][itpp]]. Reconstituted signals can be saved back to EDF source. | [[file:img/ica.png][img/ica-t.png]] | @@ -105,6 +105,10 @@ 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. +*** Score import/export + +Recordings can then be conveniently scored; scores can be imported/exported in plain ASCII. + ** SWA profiles Three kinds of SWA profiles available for Achermann model simulations: diff --git a/man/aghermann.1.in b/man/aghermann.1.in index 14b4d3c..2bf2ca9 100644 --- a/man/aghermann.1.in +++ b/man/aghermann.1.in @@ -17,8 +17,9 @@ early vs late, etc. Also provided are general-purpose facilities for displaying EEG and accompanying recordings, such as EOG and EMG, saved in EDF (European -Data Format) files. These recordings can then be conveniently scored; -scores can be imported/exported in plain ASCII. +Data Format) files (plain EDF as well as EDF+C are supported). These +recordings can then be conveniently scored; scores can be +imported/exported in plain ASCII. If run without arguments, your last session will be restored; an experiment located in \fIEXP_ROOT_DIR\fR will be selected otherwise. -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit 2db17a5ccf4da9f82be9ad8f5e2d30bae1e9d147 Author: Andrei Zavada johnhom...@gmail.com Date: Tue Apr 30 21:13:09 2013 +0300 fix LocateSelection on SF diff --git a/src/ui/sf/montage_cb.cc b/src/ui/sf/montage_cb.cc index bcb871d..572a0de 100644 --- a/src/ui/sf/montage_cb.cc +++ b/src/ui/sf/montage_cb.cc @@ -606,7 +606,7 @@ iSFPageLocateSelection_activate_cb( SF.sb_message( There is no selection in this channel); } else SF.set_cur_vpage( - SF.using_channel-selection_start / SF.using_channel-samplerate() / SF.vpagesize()); + SF.using_channel-selection_start_time / SF.vpagesize()); } -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit fb1da0b4335d9745efe7670ab4f58b9533aa83b2
Author: Andrei Zavada johnhom...@gmail.com
Date: Mon Apr 29 01:43:53 2013 +0300
sigfile::SChannel overhaul WIP
diff --git a/src/expdesign/primaries.hh b/src/expdesign/primaries.hh
index 0e18d99..e33f1cf 100644
--- a/src/expdesign/primaries.hh
+++ b/src/expdesign/primaries.hh
@@ -156,7 +156,7 @@ class CSubject : public SSubjectId {
const char*
channel() const
{
- return (_h == -1) ? (embedded) :
_source.channel_by_id(_h);
+ return (_h == -1) ? (embedded) :
_source.channel_by_id(_h).name();
}
agh::alg::SSpanfloat
page_span( size_t pagesize) const
diff --git a/src/expdesign/recording.hh b/src/expdesign/recording.hh
index 71b66fd..fe08eea 100644
--- a/src/expdesign/recording.hh
+++ b/src/expdesign/recording.hh
@@ -156,7 +156,7 @@ class CRecording {
const char* subject() const { return
_source().subject().name.c_str(); }
const char* session() const { return _source().session(); }
const char* episode() const { return _source().episode(); }
- const char* channel() const { return
_source().channel_by_id(_sig_no); }
+ const char* channel() const { return
_source().channel_by_id(_sig_no).name(); }
sigfile::SChannel::TType signal_type() const
{
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index a5244f9..021638c 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -39,9 +39,9 @@ using agh::str::tokens_trimmed;
using sigfile::CEDFFile;
template valarrayTFloat CEDFFile::get_region_original_( int, size_t, size_t)
const;
-template valarrayTFloat CEDFFile::get_region_original_( const string,
size_t, size_t) const;
+template valarrayTFloat CEDFFile::get_region_original_( const SChannel,
size_t, size_t) const;
template valarrayTFloat CEDFFile::get_region_filtered_( int, size_t, size_t)
const;
-template valarrayTFloat CEDFFile::get_region_filtered_( const string,
size_t, size_t) const;
+template valarrayTFloat CEDFFile::get_region_filtered_( const SChannel,
size_t, size_t) const;
template int CEDFFile::put_region_( int, const valarrayTFloat, size_t)
const;
template int CEDFFile::put_region_( const string, const valarrayTFloat,
size_t) const;
template int CEDFFile::export_original_( int, const string) const;
@@ -119,9 +119,6 @@ const char version_string[8] = {'0',' ',' ',' ', ' ',' ','
',' '};
}
-const char* CEDFFile::SSignal::edf_annotations_label =
-
sigfile::SChannel::kemp_signal_types[sigfile::SChannel::embedded_annotation];
-
CEDFFile::
CEDFFile (const string fname_, const int flags_)
@@ -193,7 +190,7 @@ CEDFFile (const string fname_, const int flags_)
else {
// 1. artifacts, per signal
for ( auto H : channels ) {
- ifstream thomas (make_fname_artifacts( H.label));
+ ifstream thomas (make_fname_artifacts( H.ucd));
if ( not thomas.good() )
continue;
@@ -208,7 +205,7 @@ CEDFFile (const string fname_, const int flags_)
// 2. annotations, per signal
for ( auto H : channels ) {
- ifstream fd (make_fname_annotations( H.label));
+ ifstream fd (make_fname_annotations( H.ucd));
if ( not fd.good() )
continue;
while ( fd.good() and not fd.eof() ) {
@@ -260,7 +257,7 @@ CEDFFile (const string fname_, const int flags_)
CEDFFile::
CEDFFile (const string fname_, const TSubtype subtype_, const int flags_,
- const listpairstring, size_t channels_,
+ const listpairSChannel, size_t channels_,
const size_t data_record_size_,
const size_t n_data_records_)
: CSource (fname_, flags_),
@@ -318,8 +315,9 @@ CEDFFile (const string fname_, const TSubtype subtype_,
const int flags_,
for ( auto h : channels_ ) {
auto H = channels[hi];
+ H.ucd = h.first;
strncpy( H.header.label,
-pad( H.label = h.first, 16).c_str(), 16);
+pad( H.ucd.name(), 16).c_str(), 16);
strncpy( H.header.transducer_type,
pad( H.transducer_type = no transducer info,
80).c_str(), 80);
@@ -445,19 +443,19 @@ write_ancillary_files()
{
for ( auto I : channels ) {
if ( not I.artifacts().empty() ) {
- ofstream thomas (make_fname_artifacts( I.label),
ios_base::trunc);
+ ofstream thomas (make_fname_artifacts( I.ucd),
ios_base::trunc);
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit 7bc284b5477463d89230ba04e8d5359157f9427c Author: Andrei Zavada johnhom...@gmail.com Date: Tue Apr 30 17:39:14 2013 +0300 drop some unused includes diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc index 2add6ca..55f2ca3 100644 --- a/src/libsigfile/edf.cc +++ b/src/libsigfile/edf.cc @@ -15,13 +15,10 @@ #include unistd.h #include fcntl.h #include cinttypes -#include cerrno -#include memory #include fstream #include sstream #include list #include stdexcept -#include iterator #include common/lang.hh #include common/string.hh -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit e0a68d83dacf64566502d258d068085578c764be
Author: Andrei Zavada johnhom...@gmail.com
Date: Wed May 1 02:37:07 2013 +0300
simplify ui-expdesign shortcuts in SScoringFacility::SChannel
diff --git a/src/ui/sf/channel.cc b/src/ui/sf/channel.cc
index ef1ce26..6038024 100644
--- a/src/ui/sf/channel.cc
+++ b/src/ui/sf/channel.cc
@@ -32,12 +32,10 @@ SChannel (agh::CRecording r,
SScoringFacility parent,
size_t y0,
int seq)
- : name (r.channel()),
- crecording (r),
- _h (r.F().channel_id(name)),
- filters (r.F().filters( _h)),
- annotations (r.F().annotations(_h)),
- artifacts (r.F().artifacts(_h)),
+ : crecording (r),
+ filters (r.F().filters(h())),
+ annotations (r.F().annotations(h())),
+ artifacts (r.F().artifacts(r.h())),
_p (parent),
signal_lowpass ({signal_filtered, samplerate()}),
signal_bandpass ({signal_filtered, samplerate()}),
@@ -164,7 +162,7 @@ aghui::SScoringFacility::SChannel::
get_signal_original()
{
signal_original =
- crecording.F().get_signal_original( _h);
+ crecording.F().get_signal_original( h());
// signal_original_resampled =
// sigproc::resample( signal_original, 0, signal_original.size(),
// signal_original.size() / spp());
@@ -178,7 +176,7 @@ aghui::SScoringFacility::SChannel::
get_signal_filtered()
{
signal_filtered =
- crecording.F().get_signal_filtered( _h);
+ crecording.F().get_signal_filtered( h());
// filtered is already zeromean as shipped
drop_cached_signal_properties();
}
@@ -193,7 +191,6 @@ aghui::SScoringFacility::SChannel::
in_annotations( const double time) const
{
// select this channel's annotations
- auto annotations = crecording.F().annotations(_h);
listsigfile::SAnnotation*
ret;
for ( auto A : annotations )
@@ -367,8 +364,7 @@ aghui::SScoringFacility::SChannel::
calculate_dirty_percent()
{
size_t total = 0; // in samples
- auto af = crecording.F().artifacts(_h);
- for ( auto A : af() )
+ for ( auto A : artifacts() )
total += A.size();
return percent_dirty = (float)total / n_samples();
}
@@ -397,7 +393,7 @@ detect_artifacts( const metrics::mc::SArtifactDetectionPP
P)
get_raw_profile();
// if ( this == channel currently displayed on measurements
overview )
- if ( name == _p._p.AghH() )
+ if ( strcmp( name(), _p._p.AghH()) == 0 )
_p.redraw_ssubject_timeline();
}
}
@@ -438,7 +434,7 @@ mark_flat_regions_as_artifacts( const double minsize, const
double pad)
get_mc_course();
// if ( this == channel currently displayed on measurements
overview )
- if ( name == _p._p.AghH() )
+ if ( strcmp( name(), _p._p.AghH()) == 0 )
_p.redraw_ssubject_timeline();
}
@@ -454,11 +450,11 @@ aghui::SScoringFacility::SChannel::
mark_region_as_artifact( const bool do_mark)
{
if ( do_mark )
- crecording.F().artifacts(_h).mark_artifact(
+ artifacts.mark_artifact(
selection_start_time,
selection_end_time);
else
- crecording.F().artifacts(_h).clear_artifact(
+ artifacts.clear_artifact(
selection_start_time,
selection_end_time);
@@ -473,7 +469,7 @@ mark_region_as_artifact( const bool do_mark)
get_swu_course();
get_mc_course();
- if ( name == _p._p.AghH() )
+ if ( strcmp( name(), _p._p.AghH()) == 0 )
_p.redraw_ssubject_timeline();
}
}
@@ -484,7 +480,7 @@ mark_region_as_annotation( const string label,
const sigfile::SAnnotation::TType type)
{
sigfile::mark_annotation(
- crecording.F().annotations(_h),
+ annotations,
selection_start_time, selection_end_time,
label,
type);
diff --git a/src/ui/sf/d/artifacts_cb.cc b/src/ui/sf/d/artifacts_cb.cc
index 5c0260a..027d13a 100644
--- a/src/ui/sf/d/artifacts_cb.cc
+++ b/src/ui/sf/d/artifacts_cb.cc
@@ -233,7 +233,7 @@ wSFAD_show_cb(
gtk_toggle_button_set_active( AD.bSFADPreview, FALSE);
AD.suppress_preview_handler = false;
- snprintf_buf( Artifact detection in channel %s,
SF.using_channel-name.c_str());
+ snprintf_buf( Artifact detection in channel %s,
SF.using_channel-name());
gtk_label_set_text( AD.lSFADInfo, __buf__);
snprintf_buf( %4.2f%% marked,
SF.using_channel-calculate_dirty_percent() * 100);
gtk_label_set_text(
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit f0e032bdc0bfe78067c3dda6edc6ae815ed30caa
Author: Andrei Zavada johnhom...@gmail.com
Date: Wed May 1 02:50:53 2013 +0300
lose SModelrunFacility::csubject
diff --git a/src/ui/mf/mf.cc b/src/ui/mf/mf.cc
index 37987c4..1dcf8fb 100644
--- a/src/ui/mf/mf.cc
+++ b/src/ui/mf/mf.cc
@@ -34,7 +34,6 @@ aghui::SModelrunFacility::
SModelrunFacility (agh::ach::CModelRun csim, SExpDesignUI parent)
: csimulation (csim),
// subject is known only by name, so look up his full object now
- csubject (parent.ED-subject_by_x( csim.subject())),
// not sure we need this though
display_factor (1.),
zoomed_episode (-1),
@@ -105,8 +104,9 @@ SModelrunFacility (agh::ach::CModelRun csim, SExpDesignUI
parent)
0.);
}
- snprintf_buf( Smooth: %zu, swa_smoothover);
- gtk_button_set_label( (GtkButton*)eMFSmooth, __buf__);
+ gtk_button_set_label(
+ (GtkButton*)eMFSmooth,
+ (snprintf_buf( Smooth: %zu, swa_smoothover), __buf__));
gtk_widget_show_all( (GtkWidget*)wModelrunFacility);
}
diff --git a/src/ui/mf/mf.hh b/src/ui/mf/mf.hh
index a65bb69..3fe4e34 100644
--- a/src/ui/mf/mf.hh
+++ b/src/ui/mf/mf.hh
@@ -32,8 +32,6 @@ struct SModelrunFacility {
agh::ach::CModelRun
csimulation;
- agh::CSubject
- csubject;
double cf;
double snapshot()
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 8c8e6a54ab3301e8ecee31cfba38994b21d3b921
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 30 17:25:37 2013 +0300
rip out fancy CSource channel access, only leave [int]
diff --git a/src/libsigfile/Makefile.am b/src/libsigfile/Makefile.am
index 395af14..8ddffb1 100644
--- a/src/libsigfile/Makefile.am
+++ b/src/libsigfile/Makefile.am
@@ -24,7 +24,7 @@ libsigfile_la_SOURCES := \
source.cc \
source.hh \
edf.cc \
- edf.ii \
+ edf-io.cc \
edf.hh \
page.cc \
page.hh
diff --git a/src/libsigfile/edf.ii b/src/libsigfile/edf-io.cc
similarity index 81%
rename from src/libsigfile/edf.ii
rename to src/libsigfile/edf-io.cc
index 5b2bc95..80e3b95 100644
--- a/src/libsigfile/edf.ii
+++ b/src/libsigfile/edf-io.cc
@@ -1,30 +1,23 @@
/*
- * File name: libsigfile/edf.ii
+ * File name: libsigfile/edf-io.cc
* Project: Aghermann
* Author: Andrei Zavada johnhom...@gmail.com
* Initial version: 2011-11-21
*
- * Purpose: CEDFFile (big) templated methods
+ * Purpose: CEDFFile bulk data io
*
* License: GPL
*/
+#include edf.hh
-extern template valarrayTFloat CEDFFile::get_region_original_( const int,
size_t, size_t) const;
-extern template valarrayTFloat CEDFFile::get_region_original_( const
SChannel, size_t, size_t) const;
-extern template valarrayTFloat CEDFFile::get_region_filtered_( const int,
size_t, size_t) const;
-extern template valarrayTFloat CEDFFile::get_region_filtered_( const
SChannel, size_t, size_t) const;
-extern template int CEDFFile::put_region_( const int, const
valarrayTFloat, size_t) const;
-extern template int CEDFFile::put_region_( const SChannel, const
valarrayTFloat, size_t) const;
-extern template int CEDFFile::export_original_( const int, const string)
const;
-extern template int CEDFFile::export_original_( const SChannel, const
string) const;
+using namespace std;
+using sigfile::CEDFFile;
-
-template typename A
valarrayTFloat
CEDFFile::
-get_region_original_( const A h,
- const size_t sa, const size_t sz) const
+get_region_original( const int h,
+const size_t sa, const size_t sz) const
{
if ( unlikely (_status (TStatus::bad_header | TStatus::bad_version)) )
throw invalid_argument(CEDFFile::get_region_original(): broken
source);
@@ -65,11 +58,10 @@ get_region_original_( const A h,
-template typename Th
valarrayTFloat
CEDFFile::
-get_region_filtered_( const Th h,
- const size_t smpla, const size_t smplz) const
+get_region_filtered( const int h,
+const size_t smpla, const size_t smplz) const
{
valarrayTFloat recp =
get_region_original( h, smpla, smplz);
@@ -160,12 +152,11 @@ get_region_filtered_( const Th h,
-template typename A
int
CEDFFile::
-put_region_( const A h,
-const valarrayTFloat src,
-const size_t offset) const
+put_region( const int h,
+ const valarrayTFloat src,
+ const size_t offset) const
{
if ( unlikely (_status (TStatus::bad_header | TStatus::bad_version)) )
throw invalid_argument(CEDFFile::put_region_(): broken
source);
@@ -212,21 +203,19 @@ put_region_( const A h,
-template typename Th
int
CEDFFile::
-put_signal_( const Th h,
-const valarrayTFloat src) const
+put_signal( const int h,
+ const valarrayTFloat src) const
{
- return put_region_( h, src, (size_t)0);
+ return put_region( h, src, (size_t)0);
}
-template typename Th
int
CEDFFile::
-export_original_( const Th h,
- const string fname) const
+export_original( const int h,
+const string fname) const
{
valarrayTFloat signal = get_signal_original( h);
FILE *fd = fopen( fname.c_str(), w);
@@ -240,11 +229,10 @@ export_original_( const Th h,
}
-template typename Th
int
CEDFFile::
-export_filtered_( const Th h,
- const string fname) const
+export_filtered( const int h,
+const string fname) const
{
valarrayTFloat signal = get_signal_filtered( h);
FILE *fd = fopen( fname.c_str(), w);
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index d1f7f5d..2add6ca 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -38,15 +38,6 @@ using agh::str::tokens_trimmed;
using sigfile::CEDFFile;
-template valarrayTFloat CEDFFile::get_region_original_( const int, size_t,
size_t) const;
-template valarrayTFloat CEDFFile::get_region_original_( const SChannel,
size_t, size_t) const;
-template valarrayTFloat CEDFFile::get_region_filtered_( const int, size_t,
size_t) const;
-template valarrayTFloat CEDFFile::get_region_filtered_( const SChannel,
size_t, size_t) const;
-template int CEDFFile::put_region_( const int, const valarrayTFloat,
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit c17bf95a542a5f204a7810af0222ee4175b89776 Author: Andrei Zavada johnhom...@gmail.com Date: Tue Apr 30 21:38:29 2013 +0300 update ChangeLog diff --git a/ChangeLog b/ChangeLog index 917fa7c..472ae82 100644 --- a/ChangeLog +++ b/ChangeLog @@ -17,6 +17,7 @@ v.0.9 (2013-xx-xx) settings tab. * Bind F1..3 to cycle thru profile, session and channel on measurements overview. + * Do away with separate EMG scale factor, use signal scale factor. v.0.8.2 (2013-04-07) * Fix GtkScrolledWindow issue in Annotations dialog. -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit b54694281ef70167eeae887ed87ead4d0e141e77
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 30 21:23:32 2013 +0300
talk to user if no name is given to a newly marked plain annotation
diff --git a/src/ui/sf/montage_cb.cc b/src/ui/sf/montage_cb.cc
index 572a0de..bd33190 100644
--- a/src/ui/sf/montage_cb.cc
+++ b/src/ui/sf/montage_cb.cc
@@ -1112,8 +1112,6 @@ iSFPageSelectionAnnotate_activate_cb(
if ( GTK_RESPONSE_OK ==
gtk_dialog_run( (GtkDialog*)SF.wSFAnnotationLabel) ) {
auto new_ann = gtk_entry_get_text( SF.eSFAnnotationLabel);
- if ( strlen( new_ann) == 0 )
- return;
using sigfile::SAnnotation;
auto type =
@@ -1125,6 +1123,11 @@ iSFPageSelectionAnnotate_activate_cb(
? SAnnotation::TType::eyeblink
: SAnnotation::TType::plain;
+ if ( strlen( new_ann) == 0 type == SAnnotation::TType::plain
) {
+ aghui::pop_ok_message( SF.wSF, Give a plain annotation
a name, and try again.);
+ return;
+ }
+
SF.using_channel-mark_region_as_annotation( new_ann, type);
gtk_widget_queue_draw( (GtkWidget*)SF.daSFMontage);
--
Sleep experiment manager
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit c6c25c81e8dc3dbc2e53fc8fc39bba19c086b338
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 30 02:32:03 2013 +0300
gotcha with channel selector arg passed by value
diff --git a/src/libsigfile/channel.hh b/src/libsigfile/channel.hh
index 0f61cd0..7f73e32 100644
--- a/src/libsigfile/channel.hh
+++ b/src/libsigfile/channel.hh
@@ -190,6 +190,13 @@ struct SChannel {
{
return 0 == strcasecmp( name(), rv);
}
+
+ // void operator=( const SChannel rv)
+ // {
+ // _type = rv._type;
+ // _idx = rv._idx;
+ // _custom_name = rv._custom_name;
+ // }
};
template typename C
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index 8b566b3..9d063d2 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -38,14 +38,14 @@ using agh::str::tokens_trimmed;
using sigfile::CEDFFile;
-template valarrayTFloat CEDFFile::get_region_original_( int, size_t, size_t)
const;
+template valarrayTFloat CEDFFile::get_region_original_( const int, size_t,
size_t) const;
template valarrayTFloat CEDFFile::get_region_original_( const SChannel,
size_t, size_t) const;
-template valarrayTFloat CEDFFile::get_region_filtered_( int, size_t, size_t)
const;
+template valarrayTFloat CEDFFile::get_region_filtered_( const int, size_t,
size_t) const;
template valarrayTFloat CEDFFile::get_region_filtered_( const SChannel,
size_t, size_t) const;
-template int CEDFFile::put_region_( int, const valarrayTFloat, size_t)
const;
-template int CEDFFile::put_region_( const string, const valarrayTFloat,
size_t) const;
-template int CEDFFile::export_original_( int, const string) const;
-template int CEDFFile::export_original_( const string, const string) const;
+template int CEDFFile::put_region_( const int, const valarrayTFloat,
size_t) const;
+template int CEDFFile::put_region_( const SChannel, const valarrayTFloat,
size_t) const;
+template int CEDFFile::export_original_( const int, const string) const;
+template int CEDFFile::export_original_( const SChannel, const string) const;
int
CEDFFile::
@@ -679,16 +679,14 @@ _parse_header()
string isolated_label = trim( string
(H.header.label, 16));
if ( isolated_label ==
sigfile::edf_annotations_label )
- H.ucd = sigfile::SChannel(
sigfile::SChannel::TType::embedded_annotation, 0);
+ H.ucd =
{sigfile::SChannel::TType::embedded_annotation, 0};
else {
auto tt = agh::str::tokens(
isolated_label, );
// parse legacy pre 0.9 specs (EEG F3
etc)
if ( tt.size() 1 ) {
string suggested_type =
tt.front();
- H.ucd = sigfile::SChannel
((tt.pop_front(), agh::str::join( tt, )));
- if ( suggested_type ==
H.ucd.type_s() )
- ; // all agree
- else
+ H.ucd = {(tt.pop_front(),
agh::str::join( tt, ))};
+ if ( suggested_type !=
H.ucd.type_s() )
_status |=
recognised_channel_conflicting_type;
} else {
H.ucd = sigfile::SChannel
(isolated_label);
diff --git a/src/libsigfile/edf.hh b/src/libsigfile/edf.hh
index bc7db0c..23993fc 100644
--- a/src/libsigfile/edf.hh
+++ b/src/libsigfile/edf.hh
@@ -221,9 +221,9 @@ class CEDFFile
// signal data extractors
template class Th // accommodates int or const SChannel as Th
valarrayTFloat
- get_region_original_( Th h, size_t smpla, size_t smplz) const;
+ get_region_original_( const Th h, size_t smpla, size_t smplz) const;
valarrayTFloat
- get_region_original( int h, size_t smpla, size_t smplz) const
+ get_region_original( const int h, size_t smpla, size_t smplz) const
{ return get_region_original_int( h, smpla, smplz); }
valarrayTFloat
get_region_original( const SChannel h, size_t smpla, size_t smplz)
const
@@ -231,7 +231,7 @@ class CEDFFile
template class Th
valarrayTFloat
- get_region_original_( Th h,
+ get_region_original_( const Th h,
float timea, float timez) const
{
size_t sr = samplerate(h);
@@ -239,20 +239,20 @@ class CEDFFile
h, (size_t)(timea * sr),
[med-svn] [SCM] aghermann tag, 0.9.0, created. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The tag, 0.9.0 has been created at c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f (commit) - Shortlog commit c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f Author: Andrei Zavada johnhom...@gmail.com Date: Wed May 1 03:08:39 2013 +0300 prepare 0.9.0 --- -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f Author: Andrei Zavada johnhom...@gmail.com Date: Wed May 1 03:08:39 2013 +0300 prepare 0.9.0 diff --git a/ChangeLog b/ChangeLog index 472ae82..b47e47e 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,4 +1,4 @@ -v.0.9 (2013-xx-xx) +v.0.9.0 (2013-05-01) * Parse patient_id field in EDF header and extract subject gender, DOB and id from it. * Remove Subject Info dialog; use edfhed to change EDF header. diff --git a/debian/changelog b/debian/changelog index 80ee514..d7f9dc9 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,8 @@ -aghermann (0.8.2-1) experimental; urgency=low +aghermann (0.9.0-1) experimental; urgency=low * New upstream version. - -- Andrei Zavada johnhom...@gmail.com Sun, 07 Apr 2013 19:21:16 +0200 + -- Andrei Zavada johnhom...@gmail.com Wed, 01 May 2013 02:57:16 +0200 aghermann (0.8.1-1) experimental; urgency=low -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 849128b5bab83dee4397af493342b56ed45929c4
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 30 20:37:08 2013 +0300
regression related to SScoringFacility::SChannel::type getting unused
diff --git a/src/ui/mw/mainmenu_cb.cc b/src/ui/mw/mainmenu_cb.cc
index 5137a77..5e0ba6f 100644
--- a/src/ui/mw/mainmenu_cb.cc
+++ b/src/ui/mw/mainmenu_cb.cc
@@ -309,7 +309,7 @@ iExpGloballyDetectArtifacts_activate_cb(
for ( auto SF : ED.open_scoring_facilities ) {
for ( auto H : SF-channels )
- if ( H.type == sigfile::SChannel::TType::eeg )
+ if ( H.schannel().type() ==
sigfile::SChannel::TType::eeg )
H.get_signal_filtered();
SF-queue_redraw_all();
}
@@ -374,7 +374,7 @@ iExpGloballySetFilters_activate_cb(
for ( auto SF : ED.open_scoring_facilities ) {
for ( auto H : SF-channels )
- if ( H.type == sigfile::SChannel::TType::eeg )
+ if ( H.schannel().type() ==
sigfile::SChannel::TType::eeg )
H.get_signal_filtered();
SF-queue_redraw_all();
}
diff --git a/src/ui/sf/channel.cc b/src/ui/sf/channel.cc
index a443a46..ef1ce26 100644
--- a/src/ui/sf/channel.cc
+++ b/src/ui/sf/channel.cc
@@ -144,7 +144,7 @@ SChannel (agh::CRecording r,
// don't: interchannel_gap is rubbish yet
psd.focused_band = metrics::psd::TBand::delta;
- } else if ( type == sigfile::SChannel::TType::emg )
+ } else if ( schannel().type() == sigfile::SChannel::TType::emg )
get_raw_profile();
// let it be so to avoid libconfig::readFile throwing exceptions
@@ -297,7 +297,7 @@ tuplemetrics::TType, valarrayTFloat
aghui::SScoringFacility::SChannel::
which_profile( const metrics::TType metric)
{
- switch ( type ) {
+ switch ( schannel().type() ) {
case sigfile::SChannel::TType::eeg:
switch ( metric ) {
case metrics::TType::mc:
@@ -388,7 +388,7 @@ detect_artifacts( const metrics::mc::SArtifactDetectionPP
P)
calculate_dirty_percent();
get_signal_filtered();
- if ( type == sigfile::SChannel::TType::eeg ) {
+ if ( schannel().type() == sigfile::SChannel::TType::eeg ) {
get_psd_course();
get_psd_in_bands();
get_spectrum( _p.cur_page());
@@ -430,7 +430,7 @@ mark_flat_regions_as_artifacts( const double minsize, const
double pad)
calculate_dirty_percent();
get_signal_filtered();
- if ( type == sigfile::SChannel::TType::eeg ) {
+ if ( schannel().type() == sigfile::SChannel::TType::eeg ) {
get_psd_course();
get_psd_in_bands();
get_spectrum( _p.cur_page());
@@ -466,7 +466,7 @@ mark_region_as_artifact( const bool do_mark)
get_signal_filtered();
- if ( type == sigfile::SChannel::TType::eeg ) {
+ if ( schannel().type() == sigfile::SChannel::TType::eeg ) {
get_psd_course();
get_psd_in_bands();
get_spectrum( _p.cur_page());
@@ -531,8 +531,8 @@ update_channel_menu_items( const double x)
gtk_check_menu_item_set_active( _p.iSFPageSelectionDrawEnvelope,
draw_selection_envelope);
gtk_check_menu_item_set_active( _p.iSFPageSelectionDrawDzxdf,
draw_selection_dzcdf);
- boolis_eeg = (type == sigfile::SChannel::TType::eeg),
- is_emg = (type == sigfile::SChannel::TType::emg),
+ boolis_eeg = (schannel().type() == sigfile::SChannel::TType::eeg),
+ is_emg = (schannel().type() == sigfile::SChannel::TType::emg),
have_profile = is_eeg or is_emg;
gtk_widget_set_visible( (GtkWidget*)_p.iSFPageProfilesSubmenuSeparator,
have_profile);
gtk_widget_set_visible( (GtkWidget*)_p.iiSFPageProfiles,
have_profile);
@@ -569,7 +569,7 @@ update_power_menu_items()
gtk_check_menu_item_set_active( _p.iSFPowerAutoscale,
(gboolean)autoscale_profile);
gtk_widget_set_visible( (GtkWidget*)_p.iSFPowerDrawBands,
- (type == sigfile::SChannel::TType::eeg
+ (schannel().type() ==
sigfile::SChannel::TType::eeg
draw_psd));
_p.suppress_redraw = false;
}
diff --git a/src/ui/sf/d/phasediff-construct.cc
b/src/ui/sf/d/phasediff-construct.cc
index 89d2c78..8b9a6b8 100644
--- a/src/ui/sf/d/phasediff-construct.cc
+++ b/src/ui/sf/d/phasediff-construct.cc
@@ -36,7 +36,7 @@ SPhasediffDialogWidgets (SScoringFacility SF)
// filter channels we don't have
for ( auto H : SF.channels )
- if ( H.type == sigfile::SChannel::TType::eeg ) {
+
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 7c9394f8041fd4fa1b6dc07091b6669e3f057c73
Author: andrei zavada j...@johnhommer.com
Date: Mon Apr 29 08:36:55 2013 +
WIP
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index 021638c..6bf263d 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -674,10 +674,38 @@ _parse_header()
} else {
channels.resize( n_channels);
- for ( auto H : channels )
- H.ucd = trim( string (_get_next_field(
H.header.label, 16), 16));
- // includes figuring signal type and mapping to
a canonicalised name
+ // determine validate signal types
+ for ( auto H : channels ) {
+ _get_next_field( H.header.label, 16);
+
+ if ( 0 == strcmp( H.header.label ==
sigfile::edf_annotations_label )
+H.ucd =
sigfile::SChannelsigfile::TType::embedded_annotation(0);
+ else {
+ auto tt = agh::str::tokens( H.name,
);
+ SChannel::TType figured_type;
+ // parse legacy pre 0.9 specs (EEG F3
etc)
+ if ( tt.size() 1
+(figured_type =
SChannel::figure_signal_type(tt.front().c_str()))
+!= SChannel::TType::other ) {
+ H.signal_type = figured_type;
+ H.signal_type_s = tt.front();
+ H.name = (tt.pop_front(),
agh::str::join( tt, ));
+ if ( not
H.name.follows_system1020() )
+ _status |=
non1020_channel;
+ } else {
+ H.signal_type_s =
SChannel::kemp_signal_types[
+ H.signal_type =
SChannel::signal_type_of_channel( H.name) ];
+
+ if ( not
H.label.follows_system1020() )
+ _status |=
non1020_channel;
+ if ( H.signal_type ==
SChannel::TType::other )
+ _status |=
nonkemp_signaltype;
+ }
+ }
+ H.ucd = trim( string (, 16));
+ // includes figuring signal type and mapping to
a canonicalised name
+ }
for ( auto H : channels )
H.transducer_type =
trim( string (_get_next_field(
H.header.transducer_type, 80), 80));
@@ -775,37 +803,6 @@ _parse_header()
}
- // determine validate signal types
- i = 0;
- for ( auto H : channels ) {
- if ( H.ucd.type() ==
sigfile::SChannel::TType::embedded_annotation )
- ;
- else {
- ??? move this up right after SChannel ctor
- auto tt = agh::str::tokens( H.name, );
- SChannel::TType figured_type;
- // parse legacy pre 0.9 specs (EEG F3 etc)
- if ( tt.size() 1
-(figured_type =
SChannel::figure_signal_type(tt.front().c_str()))
-!= SChannel::TType::other ) {
- H.signal_type = figured_type;
- H.signal_type_s = tt.front();
- H.name = (tt.pop_front(), agh::str::join( tt,
));
- if ( not H.name.follows_system1020() )
- _status |= non1020_channel;
- } else {
- H.signal_type_s = SChannel::kemp_signal_types[
- H.signal_type =
SChannel::signal_type_of_channel( H.name) ];
-
- if ( not H.label.follows_system1020() )
- _status |= non1020_channel;
- if ( H.signal_type == SChannel::TType::other )
- _status |= nonkemp_signaltype;
- }
- }
- ++i;
- }
-
// convenience field
_total_samples_per_record = 0;
for ( auto H : channels ) {
--
Sleep experiment manager
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit aa1164e60e5cce4c1ef040f6d227579a05b301e2
Author: Andrei Zavada johnhom...@gmail.com
Date: Mon Apr 29 01:37:04 2013 +0300
code preening
diff --git a/src/tools/edfcat.cc b/src/tools/edfcat.cc
index 45d8e1b..32d1f4b 100644
--- a/src/tools/edfcat.cc
+++ b/src/tools/edfcat.cc
@@ -194,8 +194,7 @@ make_channel_headers_for_CEDFFile( size_t n, const char
*fmt, size_t samplerate)
listpairstring, size_t ret;
for ( size_t i = 0; i n; ++i ) {
DEF_UNIQUE_CHARP (_);
- assert (asprintf( _, fmt, i) 0 );
- ret.emplace_back( _, samplerate);
+ ret.emplace_back( (ASPRINTF( _, fmt, i), _), samplerate);
}
return ret;
}
@@ -342,7 +341,7 @@ exec_convert( const SOperation::SObject obj)
sigfile::CEDFFile F ((obj + .edf).c_str(),
sigfile::CEDFFile::TSubtype::edf,
-sigfile::CTypedSource::no_ancillary_files,
+0|sigfile::CTypedSource::no_ancillary_files,
make_channel_headers_for_CEDFFile( Hh.size(),
channel%zu, obj.samplerate),
obj.record_size,
ceilf(duration / obj.record_size));
@@ -371,8 +370,8 @@ exec_prune( const SOperation::SObject obj)
for ( auto select_this : obj.channels ) {
if ( select_this = F.n_channels() ) {
DEF_UNIQUE_CHARP (_);
- assert (asprintf( _, Prune: Requested channel #%zu
(1-based) in file %s which only has %zu channel(s),
- select_this, F.filename(),
F.n_channels()) 0 );
+ ASPRINTF( _, Prune: Requested channel #%zu (1-based)
in file %s which only has %zu channel(s),
+ select_this, F.filename(), F.n_channels());
throw invalid_argument (_);
}
string label (F[select_this].header.label, 16);
diff --git a/src/ui/mw/mw.hh b/src/ui/mw/mw.hh
index d5ad5de..26e9914 100644
--- a/src/ui/mw/mw.hh
+++ b/src/ui/mw/mw.hh
@@ -178,11 +178,11 @@ class SExpDesignUI
_AghHi, _AghTi;
liststring::iterator
_AghGi, _AghDi, _AghEi;
- const char* AghH() const { return (_AghHi != AghHH.end()) ?
_AghHi-c_str() : (no channels); }
- const char* AghT() const { return (_AghTi != AghTT.end()) ?
_AghTi-c_str() : (no channels); }
- const char* AghG() const { return (_AghGi != AghGG.end()) ?
_AghGi-c_str() : (no groups); }
- const char* AghD() const { return (_AghDi != AghDD.end()) ?
_AghDi-c_str() : (no sessions); }
- const char* AghE() const { return (_AghEi != AghEE.end()) ?
_AghEi-c_str() : (no episodes); }
+ const char* AghH() const { return (_AghHi != AghHH.end()) ?
_AghHi-c_str() : (invalid channel); }
+ const char* AghT() const { return (_AghTi != AghTT.end()) ?
_AghTi-c_str() : (invalid channel); }
+ const char* AghG() const { return (_AghGi != AghGG.end()) ?
_AghGi-c_str() : (invalid group); }
+ const char* AghD() const { return (_AghDi != AghDD.end()) ?
_AghDi-c_str() : (invalid session); }
+ const char* AghE() const { return (_AghEi != AghEE.end()) ?
_AghEi-c_str() : (invalid episode); }
int AghTi() const;
int AghDi() const;
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 9c29ce116297dfd1c3df27e380c76e99065dacae
Author: Andrei Zavada johnhom...@gmail.com
Date: Mon Apr 29 01:30:13 2013 +0300
libsigfile/channel overhaul
diff --git a/src/libsigfile/channel.cc b/src/libsigfile/channel.cc
index bad547c..c7c8e69 100644
--- a/src/libsigfile/channel.cc
+++ b/src/libsigfile/channel.cc
@@ -10,79 +10,115 @@
*/
+#include map
+#include vector
#include channel.hh
using namespace std;
+using sigfile::SChannel;
+const char* sigfile::edf_annotations_label =
+ EDF Annotations;
-const char*
sigfile::SChannel::system1020_channels[sigfile::SChannel::n_channels] = { //
counted 'em all!
- Nz,
- Fp1, Fpz, Fp2,
- AF7, AF3, AFz, AF4, AF8,
- F9, F7, F5, F3, F1, Fz, F2, F4, F6, F8, F10,
- FT9, FT7, FC5, FC3, FC1, FCz, FC2, FC4, FC6, FCT8,
FT10,
- A1, T9, T7, C5, C3, C1, Cz, C2, C4, C6, T8,
T10, A2,
- TP9, TP7, CP5, CP3, CP1, CPz, CP2, CP4, CP6, TP8,
TP10,
- P9, P7, P5, P3, P1, Pz, P2, P4, P6, P8, P10,
- PO7, PO3, POz, PO4, PO8,
- O1, Oz, O2,
- Iz,
- // plus a few channels of other signal types
- Left, Right,
- Chin,
+
+namespace {
+
+const mapSChannel::TType, vectorconst char* _CT_ = {
+ {SChannel::TType::eeg,
+{(custom), // counted 'em all!
+ Nz,
+ Fp1, Fpz, Fp2,
+ AF7, AF3, AFz, AF4, AF8,
+ F9, F7, F5, F3, F1, Fz, F2, F4, F6, F8, F10,
+ FT9, FT7, FC5, FC3, FC1, FCz, FC2, FC4, FC6,
FCT8, FT10,
+ A1, T9, T7, C5, C3, C1, Cz, C2, C4, C6, T8,
T10, A2,
+ TP9, TP7, CP5, CP3, CP1, CPz, CP2, CP4, CP6, TP8,
TP10,
+ P9, P7, P5, P3, P1, Pz, P2, P4, P6, P8, P10,
+ PO7, PO3, POz, PO4, PO8,
+ O1, Oz, O2,
+ Iz,}
+ },
+ {SChannel::TType::eog,
+{(invalid),
+ Left, Right,}
+ },
+ {SChannel::TType::emg,
+{(invalid),
+ Chin,}
+ },
};
+const mapSChannel::TType, const char* _ST_ = {
+ {SChannel::TType::embedded_annotation, sigfile::edf_annotations_label},
+ {SChannel::TType::eeg, EEG},
+ {SChannel::TType::eog, EOG},
+ {SChannel::TType::emg, EMG},
+ {SChannel::TType::ecg, ECG},
+ {SChannel::TType::erg, ERG},
+ {SChannel::TType::nc , NC },
+ {SChannel::TType::meg, MEG},
+ {SChannel::TType::mcg, MCG},
+ {SChannel::TType::ep , EP },
+ {SChannel::TType::temp, Temp},
+ {SChannel::TType::resp, Resp},
+ {SChannel::TType::sao2, SaO2},
+ {SChannel::TType::light, Light},
+ {SChannel::TType::sound, Sound},
+ {SChannel::TType::event, Event},
+ {SChannel::TType::freq, Freq},
+ {SChannel::TType::other, (other)},
+};
+} // anonymous namespace
-const char*
sigfile::SChannel::kemp_signal_types[sigfile::SChannel::n_kemp_signal_types] = {
- EDF Annotations,
- EEG, EOG, EMG, ECG, ERG,
- NC, MEG, MCG, EP,
- Temp, Resp, SaO2,
- Light, Sound, Event, Freq,
- (unknown)
-};
+const char*
+SChannel::
+type_s( SChannel::TType t)
+{
+ return _ST_.at(t);
+}
-sigfile::SChannel::TType
-sigfile::SChannel::
-signal_type_of_channel( const string signal)
+template SChannel::TType t
+const char*
+SChannel::
+channel_s( int idx)
{
- size_t h = 0;
- for ( ; h = last_eeg_no; ++h )
- if ( signal == system1020_channels[h] )
- return TType::eeg;
- for ( ; h = last_eog_no; ++h )
- if ( signal == system1020_channels[h] )
- return TType::eog;
- for ( ; h = last_emg_no; ++h )
- if ( signal == system1020_channels[h] )
- return TType::emg;
- return TType::other;
+ return _CT_.at(t)[idx];
}
+namespace sigfile {
+template
+const char*
+SChannel::
+channel_sSChannel::TType::invalid(int)
+{
+ return (invalid);
+}
+}
+
+template const char* SChannel::channel_sSChannel::TType::eeg( int);
+template const char* SChannel::channel_sSChannel::TType::eog( int);
+template const char* SChannel::channel_sSChannel::TType::emg( int);
+template const char* SChannel::channel_sSChannel::TType::ecg( int);
+template const char* SChannel::channel_sSChannel::TType::erg( int);
+
+
-bool
-__attribute__ ((pure))
-sigfile::
-SChannel::operator( const SChannel rv) const
+tupleSChannel::TType, int
+figure_type_and_name( const string h)
{
- size_t ai = 0, bi = 0;
- while ( ai n_channels strcmp(c_str(), system1020_channels[ai])
)
- ++ai;
- while ( bi n_channels strcmp( rv.c_str(), system1020_channels[bi])
)
- ++bi;
- if ( ai n_channels bi n_channels ) // both are vlaid 10-20 ones:
compare by index
- return (ai bi);
- else if ( ai n_channels ) // whichever is good, wins
- return false;
- else if ( bi n_channels )
-
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 9897b3a5dca35d668820513631b2fe9b37c33642
Author: Andrei Zavada johnhom...@gmail.com
Date: Mon Apr 29 18:34:58 2013 +0300
complete 7c9394f8 (propagate all sigfile::SChannel changes throughout)
diff --git a/src/expdesign/primaries.cc b/src/expdesign/primaries.cc
index dfcafbc..09c7f46 100644
--- a/src/expdesign/primaries.cc
+++ b/src/expdesign/primaries.cc
@@ -381,7 +381,7 @@ used_samplerates( sigfile::SChannel::TType type) const
for ( auto E : D.second.episodes )
for ( auto F : E.sources )
for ( size_t h = 0; h
F().n_channels(); ++h )
- if ( type ==
sigfile::SChannel::other or
+ if ( type ==
sigfile::SChannel::TType::other or
type ==
F().signal_type(h) ) {
recp.push_back(
F().samplerate(h));
}
@@ -429,7 +429,7 @@ SEpisode (sigfile::CTypedSource F_,
auto F = sources.back();
auto HH = F().channel_list();
printf( CSubject::SEpisode::SEpisode( \%s\): %s\n,
- F().filename(), agh::str::join(HH, , ).c_str());
+ F().filename(), sigfile::join_channel_names(HH, , ).c_str());
int h = 0;
for ( auto H : HH )
recordings.insert( {H, {F, h++, fft_params, swu_params,
mc_params}});
diff --git a/src/expdesign/primaries.hh b/src/expdesign/primaries.hh
index e33f1cf..735eced 100644
--- a/src/expdesign/primaries.hh
+++ b/src/expdesign/primaries.hh
@@ -286,7 +286,7 @@ class CExpDesign {
public:
// constructor
- typedef functionvoid(const char*, size_t, size_t)
TMsmtCollectProgressIndicatorFun;
+ typedef functionvoid(const string, size_t, size_t)
TMsmtCollectProgressIndicatorFun;
CExpDesign (const string sessiondir,
TMsmtCollectProgressIndicatorFun progress_fun =
progress_fun_stdout);
~CExpDesign ()
@@ -366,7 +366,7 @@ class CExpDesign {
static bool is_supported_source( sigfile::CTypedSource);
// model runs
- int setup_modrun( const char* j, const char* d, const char* h,
+ int setup_modrun( const string j, const string d, const string h,
const SProfileParamSet,
ach::CModelRun**);
void remove_all_modruns();
@@ -382,7 +382,7 @@ class CExpDesign {
liststring enumerate_episodes() const;
listsigfile::SChannel enumerate_all_channels() const;
listsigfile::SChannel enumerate_eeg_channels() const;
- vectorsize_t used_samplerates( sigfile::SChannel::TType type =
sigfile::SChannel::other) const;
+ vectorsize_t used_samplerates( sigfile::SChannel::TType type =
sigfile::SChannel::TType::other) const;
// omp-enabled lists:foreach
typedef functionvoid(CSubject)
diff --git a/src/expdesign/recording.cc b/src/expdesign/recording.cc
index 1fe7d29..3027ac1 100644
--- a/src/expdesign/recording.cc
+++ b/src/expdesign/recording.cc
@@ -30,12 +30,7 @@ CRecording (sigfile::CTypedSource F, int sig_no,
uc_params (nullptr),
_status (0), // not computed
_source (F), _sig_no (sig_no)
-{
- // if ( F.signal_type(sig_no) == sigfile::SChannel::TType::eeg ) {
- // CBinnedPower::compute();
- // CBinnedMC::compute();
- // }
-}
+{}
agh::CRecording::
diff --git a/src/expdesign/tree-scanner.cc b/src/expdesign/tree-scanner.cc
index bd9634c..b9ba463 100644
--- a/src/expdesign/tree-scanner.cc
+++ b/src/expdesign/tree-scanner.cc
@@ -24,9 +24,9 @@ using namespace std;
namespace {
struct progress_fun_stdout_fo {
- void operator() ( const char* current, size_t n, size_t i) const
+ void operator() ( const string current, size_t n, size_t i) const
{
- printf( (%zu of %zu) %s\n, i, n, current);
+ printf( (%zu of %zu) %s\n, i, n, current.c_str());
}
};
} // namespace
@@ -391,7 +391,7 @@ compute_profiles()
size_t i, size_t total)
{
only_progress_fun(
- (string (Compute ) + R.F().filename() +
:+R.F().channel_by_id(R.h())).c_str(),
+ string (Compute ) + R.F().filename() +
:+R.F().channel_by_id(R.h()).name(),
total, i);
};
TRecordingFilterFun filter =
diff --git a/src/libsigfile/channel.cc b/src/libsigfile/channel.cc
index c7c8e69..88e960b 100644
--- a/src/libsigfile/channel.cc
+++ b/src/libsigfile/channel.cc
@@ -107,6 +107,7 @@ template const char*
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 9c53b4a28c106fd091fa7885e6bc5f67a5946a4a
Author: Andrei Zavada johnhom...@gmail.com
Date: Thu Apr 25 15:25:32 2013 +0300
new file common/containers.hh
diff --git a/src/common/Makefile.am b/src/common/Makefile.am
index 14c1b55..729016d 100644
--- a/src/common/Makefile.am
+++ b/src/common/Makefile.am
@@ -22,6 +22,7 @@ BUILT_SOURCES := \
string.hh.gch \
globals.hh.gch \
alg.hh.gch \
+ containers.hh.gch \
fs.hh.gch \
subject_id.hh.gch
diff --git a/src/common/containers.hh b/src/common/containers.hh
new file mode 100644
index 000..75d1a44
--- /dev/null
+++ b/src/common/containers.hh
@@ -0,0 +1,57 @@
+/*
+ * File name: common/containers.hh
+ * Project: Aghermann
+ * Author: Andrei Zavada johnhom...@gmail.com
+ * Initial version: 2013-04-25
+ *
+ * Purpose: misc supporting algorithms (containers)
+ *
+ * License: GPL
+ */
+
+#ifndef _AGH_COMMON_CONTAINERS_H
+#define _AGH_COMMON_CONTAINERS_H
+
+#include list
+#include forward_list
+#include vector
+
+#if HAVE_CONFIG_H !defined(VERSION)
+# include config.h
+#endif
+
+using namespace std;
+
+namespace agh {
+namespace alg {
+
+template typename T
+bool
+member( const T x, const listT v)
+{
+ return any( v.begin(), v.end(), x);
+}
+
+template typename T
+bool
+member( const T x, const forward_listT v)
+{
+ return any( v.begin(), v.end(), x);
+}
+
+template typename T
+bool
+member( const T x, const vectorT v)
+{
+ return any( v.begin(), v.end(), x);
+}
+
+} // namespace alg
+} // namespace agh
+
+#endif // _AGH_COMMON_ALG_H
+
+// Local Variables:
+// Mode: c++
+// indent-tabs-mode: 8
+// End:
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit e8d23f99f862d6028afa3c0e13ec18ab06127567
Author: Andrei Zavada johnhom...@gmail.com
Date: Thu Apr 25 14:13:02 2013 +0300
clearer code for dealing with files like Episode-2.edf in tree scanner
diff --git a/src/expdesign/tree-scanner.cc b/src/expdesign/tree-scanner.cc
index 25b88c8..42ef454 100644
--- a/src/expdesign/tree-scanner.cc
+++ b/src/expdesign/tree-scanner.cc
@@ -143,10 +143,16 @@ register_intree_source( sigfile::CTypedSource F,
d_name = (pe = next(pe), *pe),
e_name = fs::make_fname_base(*next(pe), .edf, false);
// take care of the case of episode-2.edf
- if ( e_name.size() = 3 /* strlen(a-1) */ ) {
- size_t sz = e_name.size();
- if ( e_name[sz-2] == '-' isdigit(e_name[sz-1]) )
- e_name.erase( sz-2, 2);
+ {
+ auto subf = agh::str::tokens_trimmed(e_name, -);
+ if ( subf.size() == 2 ) {
+ try {
+ stoi(subf.back());
+ e_name = subf.front();
+ } catch (...) {
+ ;
+ }
+ }
}
// refuse to register sources of wrong subjects
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit 349bcdbac211e1afe95fbe17e6bf6dd93a0e Author: Andrei Zavada johnhom...@gmail.com Date: Thu Apr 25 16:24:50 2013 +0300 ICM aborted diff --git a/src/expdesign/tree-scanner.cc b/src/expdesign/tree-scanner.cc index 6a3f0cd..bd9634c 100644 --- a/src/expdesign/tree-scanner.cc +++ b/src/expdesign/tree-scanner.cc @@ -35,9 +35,10 @@ agh::CExpDesign::TMsmtCollectProgressIndicatorFun agh::CExpDesign::progress_fun_stdout = progress_fun_stdout_fo(); - +// these old farts have been here from 2010 or earlier #define AGH_EPSEQADD_OVERLAP -1 #define AGH_EPSEQADD_TOOFAR -2 +// let them be int agh::CSubject::SEpisodeSequence:: -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit b99e718d86139c253534b244d0befe4a62794867 Author: Andrei Zavada johnhom...@gmail.com Date: Mon Apr 22 12:51:52 2013 +0300 add a ColorButton for embedded annotations diff --git a/data/mw.glade b/data/mw.glade index 78add16..edd2083 100644 --- a/data/mw.glade +++ b/data/mw.glade @@ -4517,7 +4517,7 @@ dragging individual signals with lt;igt;Altlt;/igt;.lt;/smallgt;/property property name=can_focusFalse/property property name=valignstart/property property name=border_width10/property -property name=n_rows10/property +property name=n_rows11/property property name=n_columns2/property child object class=GtkLabel id=label100 @@ -4598,8 +4598,8 @@ dragging individual signals with lt;igt;Altlt;/igt;.lt;/smallgt;/property property name=color#6b57e4d75206/property /object packing -property name=top_attach2/property -property name=bottom_attach3/property +property name=top_attach3/property +property name=bottom_attach4/property property name=x_optionsGTK_FILL/property property name=y_optionsGTK_FILL/property /packing @@ -4614,8 +4614,8 @@ dragging individual signals with lt;igt;Altlt;/igt;.lt;/smallgt;/property packing property name=left_attach1/property property name=right_attach2/property -property name=top_attach2/property -property name=bottom_attach3/property +property name=top_attach3/property +property name=bottom_attach4/property property name=y_optionsGTK_FILL/property property name=x_padding5/property /packing @@ -4633,8 +4633,8 @@ dragging individual signals with lt;igt;Altlt;/igt;.lt;/smallgt;/property property name=color#3e8e42d7/property /object packing -property name=top_attach4/property -property name=bottom_attach5/property +property name=top_attach5/property +property name=bottom_attach6/property property name=x_optionsGTK_FILL/property property name=y_optionsGTK_FILL/property /packing @@ -4649,8 +4649,8 @@ dragging individual signals with lt;igt;Altlt;/igt;.lt;/smallgt;/property packing property name=left_attach1/property property name=right_attach2/property -property name=top_attach4/property -property name=bottom_attach5/property +property name=top_attach5/property +property name=bottom_attach6/property property name=y_optionsGTK_FILL/property property name=x_padding5/property
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 5be264140f85d08add53501420dceceececbc486
Author: Andrei Zavada johnhom...@gmail.com
Date: Mon Apr 22 18:01:35 2013 +0300
suggest to hide some channels if SF being opened has too many visible ones
diff --git a/src/ui/sf/sf.cc b/src/ui/sf/sf.cc
index 991db32..10e97f8 100644
--- a/src/ui/sf/sf.cc
+++ b/src/ui/sf/sf.cc
@@ -260,6 +260,12 @@ SScoringFacility (agh::CSubject J,
(GtkContainer*)iiSFPageHidden,
item);
}
+ // if there's too many visible, suggest to hide some
+ if ( channels.size() - n_hidden 10 )
+ aghui::pop_ok_message(
+ wSF, Overcrowded montage,
+ The recording you are about to view has %zu channels.
+ You can hide some from channel context menus.,
channels.size() - n_hidden);
{
int bar_height;
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit c0feb53a99ce81bd2cb9ee7770e471218c0ed118 Author: Andrei Zavada johnhom...@gmail.com Date: Mon Apr 22 12:52:12 2013 +0300 mark embedded annotations with thick lines diff --git a/src/ui/sf/montage.cc b/src/ui/sf/montage.cc index 0714848..c86b7f9 100644 --- a/src/ui/sf/montage.cc +++ b/src/ui/sf/montage.cc @@ -786,6 +786,7 @@ draw_montage( cairo_t* cr) _p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr); + cairo_set_line_width( cr, 2.5); cairo_rectangle( cr, wa, 0, ww, da_ht); cairo_fill( cr); cairo_stroke( cr); -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit 558282eb99523dc743c8503a873a908991733741 Author: Andrei Zavada johnhom...@gmail.com Date: Mon Apr 22 23:03:28 2013 +0300 correctly apply artifact markings (regression after rel-ts work) diff --git a/src/ui/sf/channel.cc b/src/ui/sf/channel.cc index e778353..914d578 100644 --- a/src/ui/sf/channel.cc +++ b/src/ui/sf/channel.cc @@ -390,7 +390,7 @@ detect_artifacts( const metrics::mc::SArtifactDetectionPP P) metrics::mc::detect_artifacts( signal_original, samplerate(), P); for ( size_t p = 0; p marked.size(); ++p ) artifacts.mark_artifact( - marked[p] * P.scope * samplerate(), (marked[p]+1) * P.scope * samplerate()); + marked[p] * P.scope, (marked[p]+1) * P.scope); calculate_dirty_percent(); get_signal_filtered(); -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit a119f494a3a958aeb38314c84fd8232b6589c3d4 Author: Andrei Zavada johnhom...@gmail.com Date: Mon Apr 22 22:44:07 2013 +0300 move widget visibility setting calls where it was before 1160837dd diff --git a/src/ui/sf/sf.cc b/src/ui/sf/sf.cc index e01d96f..d681dac 100644 --- a/src/ui/sf/sf.cc +++ b/src/ui/sf/sf.cc @@ -223,9 +223,7 @@ SScoringFacility (agh::CSubject J, height-request, (int)da_ht, NULL); - // display proper control bar and set tooltip - gtk_widget_set_visible( (GtkWidget*)cSFScoringModeContainer, TRUE); - gtk_widget_set_visible( (GtkWidget*)cSFICAModeContainer, FALSE); + // set tooltip set_tooltip( TTipIdx::scoring_mode); // grey out phasediff button if there are fewer than 2 EEG channels @@ -284,6 +282,11 @@ SScoringFacility (agh::CSubject J, suppress_redraw = false; gtk_widget_show_all( (GtkWidget*)wSF); + + // display proper control bar (has to be done on a shown widget) + gtk_widget_set_visible( (GtkWidget*)cSFScoringModeContainer, TRUE); + gtk_widget_set_visible( (GtkWidget*)cSFICAModeContainer, FALSE); + queue_redraw_all(); // advise parent we are open -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 270ca431565d868b924a3d9b4a36d27c046a21a8
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 23 16:39:14 2013 +0300
don't decorate channels of unrecognised type
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index 21c678b..eb8002e 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -798,15 +798,11 @@ _parse_header()
H.signal_type_s = SChannel::kemp_signal_types[
H.signal_type =
SChannel::signal_type_of_channel( H.label) ];
- if ( not H.label.follows_system1020() ) { //
in case there are duplicate labels, rewrite
- DEF_UNIQUE_CHARP (_);
- ASPRINTF( _, %zu:%s, i,
H.label.c_str());
- H.label.assign( _);
+ if ( not H.label.follows_system1020() )
_status |= non1020_channel;
- }
+ if ( H.signal_type == SChannel::TType::other )
+ _status |= nonkemp_signaltype;
}
- if ( H.signal_type == SChannel::TType::other )
- _status |= nonkemp_signaltype;
}
++i;
}
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 4fc31e5e708b0aa945abf4f302f9c32bdac5c47f
Author: Andrei Zavada johnhom...@gmail.com
Date: Wed Apr 24 01:35:25 2013 +0300
update ChangeLog ICM
diff --git a/ChangeLog b/ChangeLog
index 3f57c94..fccb970 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -9,8 +9,9 @@ v.0.9 (2013-xx-xx)
* Make all timestamps in sidecar files (a) relative to recording
start, (b) expressed in seconds, to be consistent with embedded
annotations.
- * Fix crash when getting PSD on montage having channels with
+ * Fix a SF crash when getting PSD on montage having channels with
variable sample rate, on OMP-enabled hosts.
+ * Fix a SF crash with montages with ('z'-'a') channels.
v.0.8.2 (2013-04-07)
* Fix GtkScrolledWindow issue in Annotations dialog.
diff --git a/src/ui/sf/montage.cc b/src/ui/sf/montage.cc
index 56943f5..36c2cd4 100644
--- a/src/ui/sf/montage.cc
+++ b/src/ui/sf/montage.cc
@@ -761,44 +761,42 @@ draw_montage( cairo_t* cr)
}
}
// recording-wide annotations
- if ( not common_annotations.empty() ) {
- for ( auto SA : common_annotations ) {
- auto S = *SA.first;
- auto A = *SA.second;
- double cvpa = cur_xvpage_start(),
- cvpe = cur_xvpage_end(),
- evpz = cvpe - cvpa;
- double last_z = 0;
- int overlap_count = 0;
- if ( agh::alg::overlap( A.span.a, A.span.z, cvpa, cvpe)
) {
- double aa = A.span.a - cvpa,
- ae = A.span.z - cvpa;
- agh::alg::ensure_within( aa, -half_pad,
-half_pad + evpz);
- agh::alg::ensure_within( ae, -half_pad,
-half_pad + evpz);
-
- autowa = fmod(aa, evpz) / evpz * da_wd,
- ww = (ae - aa) / evpz * da_wd;
-
- if ( A.type ==
sigfile::SAnnotation::TType::plain ) {
- int disp = 0 +
- ((last_z A.span.a)
-? ++overlap_count * 5
-: (overlap_count = 0));
- last_z = A.span.z;
-
-
_p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr);
-
- cairo_set_line_width( cr, 2.5);
- cairo_rectangle( cr, wa, 0, ww, da_ht);
- cairo_fill( cr);
- cairo_stroke( cr);
+ for ( auto SA : common_annotations ) {
+ auto S = *SA.first;
+ auto A = *SA.second;
+ double cvpa = cur_xvpage_start(),
+ cvpe = cur_xvpage_end(),
+ evpz = cvpe - cvpa;
+ double last_z = 0;
+ int overlap_count = 0;
+ if ( agh::alg::overlap( A.span.a, A.span.z, cvpa, cvpe) ) {
+ double aa = A.span.a - cvpa,
+ ae = A.span.z - cvpa;
+ agh::alg::ensure_within( aa, -half_pad, -half_pad +
evpz);
+ agh::alg::ensure_within( ae, -half_pad, -half_pad +
evpz);
+
+ autowa = fmod(aa, evpz) / evpz * da_wd,
+ ww = (ae - aa) / evpz * da_wd;
+
+ if ( A.type == sigfile::SAnnotation::TType::plain ) {
+ int disp = 0 +
+ ((last_z A.span.a)
+? ++overlap_count * 5
+: (overlap_count = 0));
+ last_z = A.span.z;
+
+
_p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr);
+
+ cairo_set_line_width( cr, 2.5);
+ cairo_rectangle( cr, wa, 0, ww, da_ht);
+ cairo_fill( cr);
+ cairo_stroke( cr);
- cairo_select_font_face( cr, serif,
CAIRO_FONT_SLANT_ITALIC, CAIRO_FONT_WEIGHT_NORMAL);
- cairo_set_font_size( cr, 11);
- cairo_set_source_rgb( cr, 0., 0., 0.);
- cairo_move_to( cr, fmod(aa, evpz) /
evpz * da_wd, da_ht - 12 - disp);
- cairo_show_text( cr, A.label.c_str());
- }
+
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit ec6a8c3c302309e6f4fbe26a7e1f02d05affe773
Author: Andrei Zavada johnhom...@gmail.com
Date: Wed Apr 24 01:18:16 2013 +0300
artifacts are in seconds, in simple artifact detection code
diff --git a/src/ui/sf/channel.cc b/src/ui/sf/channel.cc
index f669e53..d463860 100644
--- a/src/ui/sf/channel.cc
+++ b/src/ui/sf/channel.cc
@@ -415,8 +415,8 @@ pairdouble, double
aghui::SScoringFacility::SChannel::
mark_flat_regions_as_artifacts( const double minsize, const double pad)
{
- size_t total_before = artifacts.total(),
- marked_here = 0;
+ double total_before = artifacts.total();
+ size_t marked_here = 0;
auto d =
sigproc::derivative( signal_original);
size_t last_j = 0;
@@ -426,10 +426,10 @@ mark_flat_regions_as_artifacts( const double minsize,
const double pad)
while ( j d.size() d[j] == 0. )
++j;
if ( j-i minsize * samplerate() ) {
- size_t extend_from = (i - last_j .1 *
samplerate()) ? last_j : i;
+ size_t extend_from = (i - last_j .1) ? last_j
: i;
artifacts.mark_artifact(
- extend_from - pad * samplerate(),
- j + pad * samplerate());
+ (double)extend_from/samplerate() - pad,
+ (double)j/samplerate() + pad);
marked_here += (j - extend_from);
last_j = j;
}
@@ -451,7 +451,7 @@ mark_flat_regions_as_artifacts( const double minsize, const
double pad)
}
return { (double)marked_here/samplerate(),
-(double)(artifacts.total() - total_before) / samplerate() };
+(double)(artifacts.total() - total_before) };
}
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit e9e19394567dfc6bded3c0957b01760a1aab1b62
Author: Andrei Zavada johnhom...@gmail.com
Date: Wed Apr 24 19:12:38 2013 +0300
have general scroll speed factor
diff --git a/src/ui/mf/mf_cb.cc b/src/ui/mf/mf_cb.cc
index 194874f..801129d 100644
--- a/src/ui/mf/mf_cb.cc
+++ b/src/ui/mf/mf_cb.cc
@@ -124,10 +124,10 @@ daMFProfile_scroll_event_cb(
switch ( event-direction ) {
case GDK_SCROLL_DOWN:
- MF.display_factor /= 1.1;
+ MF.display_factor /= MF._p.scroll_factor;
break;
case GDK_SCROLL_UP:
- MF.display_factor *= 1.1;
+ MF.display_factor *= MF._p.scroll_factor;
break;
case GDK_SCROLL_LEFT:
break;
diff --git a/src/ui/mw/mw.cc b/src/ui/mw/mw.cc
index 39c441d..35b4399 100644
--- a/src/ui/mw/mw.cc
+++ b/src/ui/mw/mw.cc
@@ -123,6 +123,7 @@ const arrayunsigned, 4
const arraydouble, 3
aghui::SExpDesignUI::FFTBinSizeValues = {{.1, .25, .5}};
+double aghui::SExpDesignUI::scroll_factor = 1.05;
using confval::SValidator;
@@ -199,6 +200,7 @@ SExpDesignUI (aghui::SSessionChooser *parent,
SValidatordouble(Profiles.PSD.FreqUpto,
active_profile_psd_freq_upto, SValidatordouble::SVFRangeIn
(0., 20.)),
SValidatordouble(Profiles.SWU.F0,
active_profile_swu_f0, SValidatordouble::SVFRangeIn
(0., 20.)),
SValidatordouble(Profiles.MC.F0,
active_profile_mc_f0, SValidatordouble::SVFRangeIn
(0., 20.)),
+ SValidatordouble(Common.ScrollFactor,
scroll_factor, SValidatordouble::SVFRangeIn
(1.001, 1.5)),
})
{
nodestroy_by_cb = true;
diff --git a/src/ui/mw/mw.hh b/src/ui/mw/mw.hh
index 5e951b0..84f1c02 100644
--- a/src/ui/mw/mw.hh
+++ b/src/ui/mw/mw.hh
@@ -300,6 +300,9 @@ class SExpDesignUI
sort_segregate;
void sort_subjects();
+ // general scrolling responsiveness
+ static double scroll_factor;
+
// _saved items
size_t tl_pph_saved,
tl_height_saved;
diff --git a/src/ui/sf/d/patterns_cb.cc b/src/ui/sf/d/patterns_cb.cc
index 723dec0..591bdf1 100644
--- a/src/ui/sf/d/patterns_cb.cc
+++ b/src/ui/sf/d/patterns_cb.cc
@@ -85,14 +85,14 @@ daSFFDThing_scroll_event_cb(
if ( event-state GDK_SHIFT_MASK )
FD.set_thing_da_width( FD.da_thing_wd + 10);
else
- FD.thing_display_scale *= 1.05;
+ FD.thing_display_scale *= FD._p._p.scroll_factor;
break;
case GDK_SCROLL_DOWN:
if ( event-state GDK_SHIFT_MASK ) {
if ( FD.da_thing_wd 20 )
FD.set_thing_da_width( FD.da_thing_wd - 10);
} else
- FD.thing_display_scale /= 1.05;
+ FD.thing_display_scale /= FD._p._p.scroll_factor;
break;
default:
break;
@@ -197,14 +197,14 @@ daSFFDField_scroll_event_cb(
if ( event-state GDK_SHIFT_MASK )
FD.set_field_da_width( FD.da_field_wd + 10);
else
- FD.field_display_scale *= 1.05;
+ FD.field_display_scale *= FD._p._p.scroll_factor;
break;
case GDK_SCROLL_DOWN:
if ( event-state GDK_SHIFT_MASK ) {
if ( FD.da_field_wd 20 )
FD.set_field_da_width( FD.da_field_wd - 10);
} else
- FD.field_display_scale /= 1.05;
+ FD.field_display_scale /= FD._p._p.scroll_factor;
break;
default:
break;
diff --git a/src/ui/sf/d/phasediff_cb.cc b/src/ui/sf/d/phasediff_cb.cc
index 9aea9ae..19bd1d1 100644
--- a/src/ui/sf/d/phasediff_cb.cc
+++ b/src/ui/sf/d/phasediff_cb.cc
@@ -47,10 +47,10 @@ daSFPD_scroll_event_cb(
switch ( event-direction ) {
case GDK_SCROLL_UP:
- PD.display_scale *= 1.05;
+ PD.display_scale *= PD._p._p.scroll_factor;
break;
case GDK_SCROLL_DOWN:
- PD.display_scale /= 1.05;
+ PD.display_scale /= PD._p._p.scroll_factor;
default:
break;
}
diff --git a/src/ui/sf/montage_cb.cc b/src/ui/sf/montage_cb.cc
index 6b3e7c4..e5109ce 100644
--- a/src/ui/sf/montage_cb.cc
+++ b/src/ui/sf/montage_cb.cc
@@ -342,7 +342,6 @@ daSFMontage_button_release_event_cb(
-#define smoothness 1.05
gboolean
daSFMontage_scroll_event_cb(
@@ -419,16 +418,16 @@ daSFMontage_scroll_event_cb(
} else {
switch ( event-direction ) {
case GDK_SCROLL_DOWN:
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit f315f3b8cb781458d7c452a87668b36ea2e7fc2b
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 23 23:27:33 2013 +0300
clear up display scale calibration
diff --git a/src/ui/sf/sf.cc b/src/ui/sf/sf.cc
index 6f306c1..941330d 100644
--- a/src/ui/sf/sf.cc
+++ b/src/ui/sf/sf.cc
@@ -159,44 +159,48 @@ SScoringFacility (agh::CSubject J,
estimate_montage_height();
for ( auto h : channels ) {
- if ( not isfinite(h.signal_display_scale) ||
-!agh::alg::value_within( h.signal_display_scale, 0., 1e-9)
)
+ if ( not isfinite(h.signal_display_scale) )
h.signal_display_scale =
agh::alg::calibrate_display_scale(
h.signal_filtered,
vpagesize() * h.samplerate() * min
(h.crecording.total_pages(), (size_t)10),
interchannel_gap / 2);
+ agh::alg::ensure_within( h.signal_display_scale, 1e-9, 1e9);
+
if ( h.type == sigfile::SChannel::TType::eeg ) {
// calibrate profile display scales
- if ( not isfinite(h.psd.display_scale) ||
-!agh::alg::value_within( h.psd.display_scale, 0.,
1e-9) )
+ if ( not isfinite(h.psd.display_scale) )
h.psd.display_scale =
agh::alg::calibrate_display_scale(
h.psd.course_in_bands[metrics::psd::TBand::delta],
h.psd.course.size(),
interchannel_gap / 4);
- if ( not isfinite(h.mc.display_scale) ||
-!agh::alg::value_within( h.mc.display_scale, 0.,
1e-9) )
+ agh::alg::ensure_within( h.psd.display_scale, 1e-9,
1e9);
+
+ if ( not isfinite(h.mc.display_scale) )
h.mc.display_scale =
agh::alg::calibrate_display_scale(
h.mc.course,
h.mc.course.size(),
interchannel_gap / 4);
- if ( not isfinite(h.swu.display_scale) ||
-!agh::alg::value_within( h.swu.display_scale, 0.,
1e-9) )
+ agh::alg::ensure_within( h.mc.display_scale, 1e-9, 1e9);
+
+ if ( not isfinite(h.swu.display_scale) )
h.swu.display_scale =
agh::alg::calibrate_display_scale(
h.swu.course,
h.swu.course.size(),
interchannel_gap / 4);
+ agh::alg::ensure_within( h.swu.display_scale, 1e-9,
1e9);
+
} else if ( h.type == sigfile::SChannel::TType::emg ) {
- if ( not isfinite(h.emg_display_scale) ||
-!agh::alg::value_within( h.emg_display_scale, 0.,
1e-9) )
+ if ( not isfinite(h.emg_display_scale) )
h.emg_display_scale =
agh::alg::calibrate_display_scale(
h.raw_profile,
h.raw_profile.size(),
interchannel_gap / 4);
+ agh::alg::value_within( h.emg_display_scale, 1e-9, 1e9);
}
h._put_selection();
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 61a2f27252d1c0ec065738397d901a89f1161c5c
Author: Andrei Zavada johnhom...@gmail.com
Date: Wed Apr 24 01:04:19 2013 +0300
deal with ('z'-'a') channels
and use using to shorten lines
diff --git a/src/ui/sf/channel.cc b/src/ui/sf/channel.cc
index 914d578..f669e53 100644
--- a/src/ui/sf/channel.cc
+++ b/src/ui/sf/channel.cc
@@ -25,11 +25,13 @@ pattern::SPatternPPackTFloat
aghui::SScoringFacility::SChannel::pattern_params =
{.25, 0., 1.5, 1, .1, .5, 3};
+using confval::SValidator;
+
aghui::SScoringFacility::SChannel::
-SChannel( agh::CRecording r,
+SChannel (agh::CRecording r,
SScoringFacility parent,
size_t y0,
- char seq)
+ int seq)
: name (r.channel()),
type (r.signal_type()),
crecording (r),
@@ -66,35 +68,35 @@ SChannel( agh::CRecording r,
draw_phasic_eyeblink (true),
apply_reconstituted (false),
config_keys_b ({
- confval::SValidatorbool( string(1, seq) + .hidden,
hidden),
- confval::SValidatorbool( string(1, seq) + .draw_zeroline,
draw_zeroline),
- confval::SValidatorbool( string(1, seq) +
.draw_original_signal,draw_original_signal),
- confval::SValidatorbool( string(1, seq) +
.draw_filtered_signal,draw_filtered_signal),
- confval::SValidatorbool( string(1, seq) + .draw_emg,
draw_emg),
- confval::SValidatorbool( string(1, seq) + .draw_psd,
draw_psd),
- confval::SValidatorbool( string(1, seq) + .draw_swu,
draw_swu),
- confval::SValidatorbool( string(1, seq) + .draw_psd_bands,
draw_psd_bands),
- confval::SValidatorbool( string(1, seq) + .draw_spectrum,
draw_spectrum),
- confval::SValidatorbool( string(1, seq) + .draw_mc,
draw_mc),
- confval::SValidatorbool( string(1, seq) +
.draw_phasic_spindle, draw_phasic_spindle),
- confval::SValidatorbool( string(1, seq) +
.draw_phasic_Kcomplex,draw_phasic_Kcomplex),
- confval::SValidatorbool( string(1, seq) +
.draw_phasic_eyeblink,draw_phasic_eyeblink),
- confval::SValidatorbool( string(1, seq) +
.autoscale_profile, autoscale_profile),
- confval::SValidatorbool( string(1, seq) + .resample_signal,
resample_signal),
- confval::SValidatorbool( string(1, seq) + .resample_power,
resample_power),
- confval::SValidatorbool( string(1, seq) +
.draw_selection_course, draw_selection_course),
- confval::SValidatorbool( string(1, seq) +
.draw_selection_envelope, draw_selection_envelope),
- confval::SValidatorbool( string(1, seq) +
.draw_selection_dzcdf,draw_selection_dzcdf),
+ SValidatorbool( string(h)+to_string(seq) + .hidden,
hidden),
+ SValidatorbool( string(h)+to_string(seq) +
.draw_zeroline,draw_zeroline),
+ SValidatorbool( string(h)+to_string(seq) +
.draw_original_signal, draw_original_signal),
+ SValidatorbool( string(h)+to_string(seq) +
.draw_filtered_signal, draw_filtered_signal),
+ SValidatorbool( string(h)+to_string(seq) + .draw_emg,
draw_emg),
+ SValidatorbool( string(h)+to_string(seq) + .draw_psd,
draw_psd),
+ SValidatorbool( string(h)+to_string(seq) + .draw_swu,
draw_swu),
+ SValidatorbool( string(h)+to_string(seq) +
.draw_psd_bands, draw_psd_bands),
+ SValidatorbool( string(h)+to_string(seq) +
.draw_spectrum,draw_spectrum),
+ SValidatorbool( string(h)+to_string(seq) + .draw_mc,
draw_mc),
+ SValidatorbool( string(h)+to_string(seq) +
.draw_phasic_spindle, draw_phasic_spindle),
+ SValidatorbool( string(h)+to_string(seq) +
.draw_phasic_Kcomplex, draw_phasic_Kcomplex),
+ SValidatorbool( string(h)+to_string(seq) +
.draw_phasic_eyeblink, draw_phasic_eyeblink),
+ SValidatorbool( string(h)+to_string(seq) +
.autoscale_profile,autoscale_profile),
+ SValidatorbool( string(h)+to_string(seq) +
.resample_signal, resample_signal),
+ SValidatorbool( string(h)+to_string(seq) +
.resample_power, resample_power),
+ SValidatorbool( string(h)+to_string(seq) +
.draw_selection_course,draw_selection_course),
+ SValidatorbool( string(h)+to_string(seq) +
.draw_selection_envelope, draw_selection_envelope),
+ SValidatorbool( string(h)+to_string(seq) +
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 78da140c73c1612ea1adb5a8824e62326c99d368
Author: Andrei Zavada johnhom...@gmail.com
Date: Wed Apr 24 19:11:44 2013 +0300
rename some vars, reindent some
diff --git a/src/expdesign/primaries.cc b/src/expdesign/primaries.cc
index bebb923..c5e478f 100644
--- a/src/expdesign/primaries.cc
+++ b/src/expdesign/primaries.cc
@@ -369,11 +369,11 @@ enumerate_all_channels() const
}
-listsize_t
+vectorsize_t
agh::CExpDesign::
used_samplerates( sigfile::SChannel::TType type) const
{
- listsize_t recp;
+ vectorsize_t recp;
for ( auto G : groups )
for ( auto J : G.second )
for ( auto D : J.measurements )
@@ -384,8 +384,8 @@ used_samplerates( sigfile::SChannel::TType type) const
type ==
F().signal_type(h) ) {
recp.push_back(
F().samplerate(h));
}
- recp.sort();
- recp.unique();
+ sort(recp.begin(), recp.end());
+ unique(recp.begin(), recp.end());
return recp;
}
diff --git a/src/expdesign/primaries.hh b/src/expdesign/primaries.hh
index d90798a..6ab0dcd 100644
--- a/src/expdesign/primaries.hh
+++ b/src/expdesign/primaries.hh
@@ -381,7 +381,7 @@ class CExpDesign {
liststring enumerate_episodes() const;
listsigfile::SChannel enumerate_all_channels() const;
listsigfile::SChannel enumerate_eeg_channels() const;
- listsize_t used_samplerates( sigfile::SChannel::TType type =
sigfile::SChannel::other) const;
+ vectorsize_t used_samplerates( sigfile::SChannel::TType type =
sigfile::SChannel::other) const;
// omp-enabled lists:foreach
typedef functionvoid(CSubject)
diff --git a/src/ui/mw/measurements.cc b/src/ui/mw/measurements.cc
index 9a77170..566cd3a 100644
--- a/src/ui/mw/measurements.cc
+++ b/src/ui/mw/measurements.cc
@@ -46,9 +46,10 @@ aghui::SExpDesignUI::SSubjectPresentation::
draw_timeline( const char *fname) const
{
cairo_surface_t *cs =
- cairo_svg_surface_create( fname,
- timeline_width() + tl_left_margin() +
tl_right_margin(),
- timeline_height());
+ cairo_svg_surface_create(
+ fname,
+ tl_width() + tl_left_margin() + tl_right_margin(),
+ tl_height());
cairo_t *cr = cairo_create( cs);
draw_timeline( cr);
cairo_destroy( cr);
@@ -62,16 +63,17 @@ draw_timeline( cairo_t *cr) const
{
bool have_episodes = cprofile not cprofile-mm_list().empty();
- if ( not have_episodes ) {
- aghui::cairo_put_banner( cr, 400, timeline_height(), (no
episodes), 24);
- }
+ if ( not have_episodes )
+ aghui::cairo_put_banner(
+ cr, 400, tl_height(), (no episodes), 24);
if ( have_episodes ) {
// day and night
{
cairo_pattern_t *cp =
- cairo_pattern_create_linear( tl_left_margin(),
0.,
-timeline_width() -
tl_right_margin(), 0.);
+ cairo_pattern_create_linear(
+ tl_left_margin(), 0.,
+ tl_width() - tl_right_margin(), 0.);
struct tm clock_time;
memcpy( clock_time, localtime( _p._p.timeline_start),
sizeof(clock_time));
clock_time.tm_hour = 4;
@@ -82,9 +84,11 @@ draw_timeline( cairo_t *cr) const
for ( t = dawn; t timeline_end(); t += 3600 * 12, day
= !day )
if ( t timeline_start() )
_p._p.CwB[day ? TColour::mw_day :
TColour::mw_night].
- pattern_add_color_stop_rgba(
cp, (double)_p._p.T2P(t) / timeline_width());
+ pattern_add_color_stop_rgba(
+ cp,
(double)_p._p.T2P(t) / tl_width());
cairo_set_source( cr, cp);
- cairo_rectangle( cr, tl_left_margin(), 0.,
tl_left_margin() + timeline_width(), timeline_height());
+ cairo_rectangle( cr, tl_left_margin(), 0.,
+tl_left_margin() + tl_width(),
tl_height());
cairo_fill( cr);
cairo_stroke( cr);
cairo_pattern_destroy( cp);
@@ -116,7 +120,7 @@ draw_timeline( cairo_t *cr) const
_p._p.CwB[TColour::mw_profile].set_source_rgba( cr);
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 6fc0805e8e86b2cef1df5bdca409ee0a14fed144
Author: Andrei Zavada johnhom...@gmail.com
Date: Thu Apr 25 15:28:28 2013 +0300
clarify CTypedSource::TType values (subsume edfplus into edf)
diff --git a/src/libsigfile/source.cc b/src/libsigfile/source.cc
index 6aa74f0..b63ded3 100644
--- a/src/libsigfile/source.cc
+++ b/src/libsigfile/source.cc
@@ -28,9 +28,6 @@ CTypedSource (const string fname,
case TType::edf:
_obj = new CEDFFile( fname, flags);
break;
- case TType::edfplus:
- //_obj = new CEDFPlusFile( fname);
- break;
case TType::unrecognised:
throw invalid_argument (Unrecognised source type);
}
@@ -63,10 +60,6 @@ CTypedSource (CTypedSource rv)
case TType::edf:
_obj = new CEDFFile( move(*(CEDFFile*)rv._obj));
break;
- case TType::edfplus:
- //_obj = new CEDFPlusFile( *static_castCEDFPlusFile*(rv._obj);
- throw invalid_argument (Source type 'edf+' not yet supported);
- break;
case TType::unrecognised:
throw invalid_argument (Unrecognised source type);
default:
diff --git a/src/libsigfile/source.hh b/src/libsigfile/source.hh
index 449269a..98aed9d 100644
--- a/src/libsigfile/source.hh
+++ b/src/libsigfile/source.hh
@@ -37,7 +37,7 @@ class CTypedSource
enum class TType : int {
unrecognised,
bin, ascii,
- edf, edfplus,
+ edf,
};
private:
diff --git a/src/ui/mw/admit-one.cc b/src/ui/mw/admit-one.cc
index 4b392f2..bb7ef16 100644
--- a/src/ui/mw/admit-one.cc
+++ b/src/ui/mw/admit-one.cc
@@ -30,7 +30,6 @@ dnd_maybe_admit_one( const char* fname)
Fp = new CTypedSource (fname, ED-fft_params.pagesize);
switch ( Fp-type() ) {
case CTypedSource::TType::edf:
- case CTypedSource::TType::edfplus:
{
CEDFFile F = *static_castCEDFFile* ((*Fp)());
if ( F.subtype() == CEDFFile::TSubtype::edfplus_d ) {
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit c804ec2a70de61b0606f28702cf840e9df949011
Author: Andrei Zavada johnhom...@gmail.com
Date: Thu Apr 25 15:27:05 2013 +0300
discard and report unsupported files early in tree scanner
diff --git a/src/expdesign/primaries.hh b/src/expdesign/primaries.hh
index 6ab0dcd..12861c9 100644
--- a/src/expdesign/primaries.hh
+++ b/src/expdesign/primaries.hh
@@ -363,6 +363,7 @@ class CExpDesign {
// edf sources
int register_intree_source( sigfile::CTypedSource,
const char **reason_if_failed_p = nullptr);
+ static bool is_supported_source( sigfile::CTypedSource);
// model runs
int setup_modrun( const char* j, const char* d, const char* h,
diff --git a/src/expdesign/tree-scanner.cc b/src/expdesign/tree-scanner.cc
index 42ef454..6a3f0cd 100644
--- a/src/expdesign/tree-scanner.cc
+++ b/src/expdesign/tree-scanner.cc
@@ -240,8 +240,17 @@ register_intree_source( sigfile::CTypedSource F,
-
-
+bool
+agh::CExpDesign::
+is_supported_source( sigfile::CTypedSource F)
+{
+ using namespace sigfile;
+ CEDFFile::TSubtype subtype;
+ return F.type() == CTypedSource::TType::edf and
+ (subtype = static_castCEDFFile*(F()) - subtype(),
+(subtype == CEDFFile::TSubtype::edf ||
+ subtype == CEDFFile::TSubtype::edfplus_c));
+}
namespace {
@@ -264,11 +273,16 @@ edf_file_processor( const char *fname, const struct
stat*, int flag, struct FTW
++__cur_edf_file;
only_progress_fun( fname, agh::fs::__n_edf_files,
__cur_edf_file);
try {
- sigfile::CTypedSource f_tmp {fname,
__expdesign-fft_params.pagesize};
- string st = f_tmp().explain_status();
+ using namespace sigfile;
+ CTypedSource F {fname,
__expdesign-fft_params.pagesize};
+ string st = F().explain_status();
if ( not st.empty() )
__expdesign-log_message( In
%s:\n%s\n, fname, st.c_str());
- __expdesign - register_intree_source(
move(f_tmp));
+ // we only support edf and edfplus/edf_c
+ if ( agh::CExpDesign::is_supported_source(F) )
+ __expdesign - register_intree_source(
move(F));
+ else
+ __expdesign - log_message( File %s:
unsupported format\n, fname);
} catch ( invalid_argument ex) {
__expdesign-log_message(ex.what());
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit d267babf9d107458c8a81ab55b0b63badd155acf
Author: Andrei Zavada johnhom...@gmail.com
Date: Fri Apr 26 01:47:01 2013 +0300
improve drawing of annotations on hypnogram
diff --git a/src/ui/sf/hypnogram.cc b/src/ui/sf/hypnogram.cc
index 2ce9104..47ff34a 100644
--- a/src/ui/sf/hypnogram.cc
+++ b/src/ui/sf/hypnogram.cc
@@ -76,7 +76,7 @@ draw_hypnogram( cairo_t *cr)
// extra: annotations
{
- _p.CwB[SExpDesignUI::TColour::sf_annotations].set_source_rgba(
cr);
+ _p.CwB[SExpDesignUI::TColour::sf_annotations].set_source_rgba(
cr, .9);
cairo_set_line_width( cr, 18.);
auto total_seconds = total_pages() * pagesize();
@@ -87,6 +87,15 @@ draw_hypnogram( cairo_t *cr)
}
}
cairo_stroke( cr);
+
+
_p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr, .9);
+ for ( auto SA : common_annotations ) {
+ auto A = *SA.second;
+ cairo_move_to( cr, A.span.a / total_seconds * da_wd -
1, 4); // extend by one pixel to prevent
+ cairo_line_to( cr, A.span.z / total_seconds * da_wd +
1, 4); // zero-length annotations to vanish
+ }
+
+ cairo_stroke( cr);
}
// extra: artifacts
@@ -97,8 +106,8 @@ draw_hypnogram( cairo_t *cr)
auto total_seconds = total_pages() * pagesize();
for ( auto H : channels ) {
for ( auto A : H.artifacts() ) {
- cairo_move_to( cr, A.a / total_seconds * da_wd,
12);
- cairo_line_to( cr, A.z / total_seconds * da_wd,
12);
+ cairo_move_to( cr, A.a / total_seconds * da_wd
- 1, 12);
+ cairo_line_to( cr, A.z / total_seconds * da_wd
+ 1, 12);
}
}
cairo_stroke( cr);
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 7d227527e5b93304125c9f4a98619eed9a3bc337
Author: Andrei Zavada johnhom...@gmail.com
Date: Thu Apr 25 01:49:50 2013 +0300
expose a double scroll_factor and bool suppress_scan_report
diff --git a/data/mw-dialogs.glade b/data/mw-dialogs.glade
index 6d38469..01db660 100644
--- a/data/mw-dialogs.glade
+++ b/data/mw-dialogs.glade
@@ -2486,7 +2486,7 @@ With bug reports, either send yours to lt;a
href=mailto:aghermann-users@lists.
property name=can_focusFalse/property
property name=xalign0/property
property name=ypad8/property
-property name=label
translatable=yeslt;bgt;lt;biggt;Recordings not
includedlt;/biggt;lt;/bgt;/property
+property name=label translatable=yeslt;bgt;lt;biggt;Tree
scan reportlt;/biggt;lt;/bgt;/property
property name=use_markupTrue/property
/object
packing
diff --git a/data/mw.glade b/data/mw.glade
index 3fdfc20..3e904f8 100644
--- a/data/mw.glade
+++ b/data/mw.glade
@@ -397,6 +397,12 @@
property name=step_increment0.01/property
property name=page_increment0.10001/property
/object
+ object class=GtkAdjustment id=jScrollSpeedFactor
+property name=lower1.0009/property
+property name=upper2/property
+property name=step_increment0.01/property
+property name=page_increment0.10001/property
+ /object
object class=GtkAdjustment id=jUltradianCycleDetectionAccuracy
property name=lower0.5/property
property name=upper20/property
@@ -1507,20 +1513,11 @@ rm */*/*/.*.{psd,mc,swu}/property
property name=halignstart/property
property name=valignstart/property
property name=border_width20/property
-property name=n_rows3/property
+property name=n_rows2/property
property name=n_columns3/property
property name=column_spacing40/property
property name=row_spacing40/property
child
- placeholder/
-/child
-child
- placeholder/
-/child
-child
- placeholder/
-/child
-child
object class=GtkFrame id=fScoreCodes
property name=visibleTrue/property
property name=can_focusFalse/property
@@ -1811,8 +1808,8 @@ rm */*/*/.*.{psd,mc,swu}/property
/child
/object
packing
-property name=left_attach1/property
-property name=right_attach2/property
+property name=left_attach2/property
+property name=right_attach3/property
property
name=x_optionsGTK_FILL/property
property
name=y_optionsGTK_FILL/property
/packing
@@ -1832,16 +1829,13 @@ rm */*/*/.*.{psd,mc,swu}/property
property
name=can_focusFalse/property
property
name=border_width10/property
property name=n_rows3/property
-property name=n_columns3/property
+property name=n_columns2/property
property
name=column_spacing10/property
property
name=row_spacing10/property
child
placeholder/
/child
child
- placeholder/
-/child
-child
object class=GtkLabel id=label2
property
name=visibleTrue/property
property
name=can_focusFalse/property
@@ -1881,15 +1875,12 @@ rm */*/*/.*.{psd,mc,swu}/property
/attributes
/object
packing
-property
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit a2b839bc4b127e42273723f97c20dc24ea3f2f69
Author: Andrei Zavada johnhom...@gmail.com
Date: Fri Apr 26 17:10:54 2013 +0300
apply smarter label stacking from b8a4a86be3 for channel annotations, too
diff --git a/src/ui/sf/montage.cc b/src/ui/sf/montage.cc
index 8e892cf..ce882df 100644
--- a/src/ui/sf/montage.cc
+++ b/src/ui/sf/montage.cc
@@ -481,8 +481,13 @@ draw_page( cairo_t *cr,
// annotations
if ( _p.mode == aghui::SScoringFacility::TMode::scoring
and not annotations.empty() ) {
- double last_z = 0;
+ double last_label_end = 0;
int overlap_count = 0;
+
+ cairo_select_font_face( cr, serif, CAIRO_FONT_SLANT_ITALIC,
CAIRO_FONT_WEIGHT_NORMAL);
+ cairo_set_font_size( cr, 11);
+ cairo_text_extents_t extents;
+
for ( auto A : annotations ) {
if ( agh::alg::overlap( A.span.a, A.span.z, cvpa, cvpe)
) {
double aa = A.span.a - cvpa,
@@ -494,11 +499,13 @@ draw_page( cairo_t *cr,
ww = (ae - aa) / evpz * wd;
if ( A.type ==
sigfile::SAnnotation::TType::plain ) {
+ cairo_text_extents( cr,
A.label.c_str(), extents);
int disp = ptop +
- ((last_z A.span.a)
-? ++overlap_count * 5
+ ((last_label_end wa)
+? ++overlap_count * 12
: (overlap_count = 0));
- last_z = A.span.z;
+ last_label_end = max( wa +
extents.width + 3, last_label_end);
+
cairo_pattern_t *cp =
cairo_pattern_create_linear( 0., disp, 0., pbot);
_p._p.CwB[SExpDesignUI::TColour::sf_annotations].pattern_add_color_stop_rgba(
cp, 0., 1.);
_p._p.CwB[SExpDesignUI::TColour::sf_annotations].pattern_add_color_stop_rgba(
cp, .1, 0.3);
@@ -510,11 +517,10 @@ draw_page( cairo_t *cr,
cairo_stroke( cr);
cairo_pattern_destroy( cp);
- cairo_select_font_face( cr, serif,
CAIRO_FONT_SLANT_ITALIC, CAIRO_FONT_WEIGHT_NORMAL);
- cairo_set_font_size( cr, 11);
cairo_set_source_rgb( cr, 0., 0., 0.);
cairo_move_to( cr, fmod(aa, evpz) /
evpz * wd, disp + 12);
cairo_show_text( cr, A.label.c_str());
+ cairo_stroke( cr);
} else if ( A.type ==
sigfile::SAnnotation::TType::phasic_event_spindle
and draw_phasic_spindle ) {
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit b8a4a86be37515d3f320d42eeca3077cebf0cb4d Author: Andrei Zavada johnhom...@gmail.com Date: Fri Apr 26 16:49:15 2013 +0300 more accurate stacking of overlapping embedded annotation labels diff --git a/src/ui/sf/montage.cc b/src/ui/sf/montage.cc index 67af5e7..8e892cf 100644 --- a/src/ui/sf/montage.cc +++ b/src/ui/sf/montage.cc @@ -791,7 +791,7 @@ draw_montage( cairo_t* cr) (last_label_end wa) ? ++overlap_count * 12 : (overlap_count = 0); - last_label_end = wa + extents.width + 3; + last_label_end = max( wa + extents.width + 3, last_label_end); _p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr, .9); cairo_set_line_width( cr, 2.5); -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 52fad311dd8266026cb5ebcbf8f07bac73171fb1
Author: Andrei Zavada johnhom...@gmail.com
Date: Sat Apr 27 14:33:12 2013 +0300
correctly handle last_used_version wrt changelog popup
diff --git a/src/expdesign/primaries.cc b/src/expdesign/primaries.cc
index 695a110..dfcafbc 100644
--- a/src/expdesign/primaries.cc
+++ b/src/expdesign/primaries.cc
@@ -115,7 +115,8 @@ CExpDesign (const string session_dir_,
if ( last_used_version != VERSION ) {
printf( Purging old files as we are upgrading from version %s
to %s\n, last_used_version.c_str(), VERSION);
}
- last_used_version = VERSION;
+ // last_used_version = VERSION;
+ /// leave it so SExpDesignUI::populate will see it and pop the changelog
scan_tree( progress_fun);
}
diff --git a/src/ui/mw/populate.cc b/src/ui/mw/populate.cc
index 60b055b..f156a29 100644
--- a/src/ui/mw/populate.cc
+++ b/src/ui/mw/populate.cc
@@ -71,10 +71,12 @@ populate( bool do_load)
gtk_window_set_title( wMainWindow,
(string (Aghermann: ) +
agh::str::homedir2tilda( ED-session_dir())).c_str());
+
if ( ED-last_used_version != VERSION ) {
printf( Upgrading from version %s, here's ChangeLog for
you\n, ED-last_used_version.c_str());
show_changelog();
}
+ ED-last_used_version = VERSION;
snprintf_buf( Smooth: %zu, smooth_profile);
gtk_button_set_label( (GtkButton*)eMsmtProfileSmooth, __buf__);
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit eceb9941250fe2c1deb436e874bd3b93d587bc1e
Author: Andrei Zavada johnhom...@gmail.com
Date: Fri Apr 26 01:49:49 2013 +0300
better, but still not optimal, stacking of ann. labels on montage
diff --git a/src/ui/sf/montage.cc b/src/ui/sf/montage.cc
index 71fb38d..67af5e7 100644
--- a/src/ui/sf/montage.cc
+++ b/src/ui/sf/montage.cc
@@ -761,44 +761,53 @@ draw_montage( cairo_t* cr)
}
}
// recording-wide annotations
- for ( auto SA : common_annotations ) {
- auto S = *SA.first;
- auto A = *SA.second;
+ if ( not common_annotations.empty() ) {
+ cairo_select_font_face( cr, serif, CAIRO_FONT_SLANT_ITALIC,
CAIRO_FONT_WEIGHT_NORMAL);
+ cairo_set_font_size( cr, 10);
+ cairo_text_extents_t extents;
+
+ double last_label_end = 0.;
+ int overlap_count = 0;
+
double cvpa = cur_xvpage_start(),
cvpe = cur_xvpage_end(),
evpz = cvpe - cvpa;
- double last_z = 0;
- int overlap_count = 0;
- if ( agh::alg::overlap( A.span.a, A.span.z, cvpa, cvpe) ) {
- double aa = A.span.a - cvpa,
- ae = A.span.z - cvpa;
- agh::alg::ensure_within( aa, -half_pad, -half_pad +
evpz);
- agh::alg::ensure_within( ae, -half_pad, -half_pad +
evpz);
-
- autowa = fmod(aa, evpz) / evpz * da_wd,
- ww = (ae - aa) / evpz * da_wd;
-
- int disp = 0 +
- ((last_z A.span.a)
-? ++overlap_count * 5
-: (overlap_count = 0));
- last_z = A.span.z;
-
-
_p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr, .9);
- cairo_set_line_width( cr, 2.5);
- cairo_rectangle( cr, wa, 0, ww, da_ht);
- cairo_stroke( cr);
-
_p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr);
- cairo_rectangle( cr, wa, 0, ww, da_ht);
- cairo_fill( cr);
- cairo_stroke( cr);
+ for ( auto SA : common_annotations ) {
+ auto S = *SA.first;
+ auto A = *SA.second;
+ if ( agh::alg::overlap( A.span.a, A.span.z, cvpa, cvpe)
) {
+ double aa = A.span.a - cvpa,
+ ae = A.span.z - cvpa;
+ agh::alg::ensure_within( aa, -half_pad,
-half_pad + evpz);
+ agh::alg::ensure_within( ae, -half_pad,
-half_pad + evpz);
- cairo_select_font_face( cr, serif,
CAIRO_FONT_SLANT_ITALIC, CAIRO_FONT_WEIGHT_NORMAL);
- cairo_set_font_size( cr, 11);
- cairo_set_source_rgb( cr, 0., 0., 0.);
- cairo_move_to( cr, fmod(aa, evpz) / evpz * da_wd, da_ht
- 12 - disp);
- cairo_show_text( cr, A.label.c_str());
+ autowa = fmod(aa, evpz) / evpz * da_wd,
+ ww = (ae - aa) / evpz * da_wd;
+
+ cairo_text_extents( cr, A.label.c_str(),
extents);
+
+ int disp = 0 +
+ (last_label_end wa)
+ ? ++overlap_count * 12
+ : (overlap_count = 0);
+ last_label_end = wa + extents.width + 3;
+
+
_p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr, .9);
+ cairo_set_line_width( cr, 2.5);
+ cairo_rectangle( cr, wa, 0, ww, da_ht);
+ cairo_stroke( cr);
+
+
_p.CwB[SExpDesignUI::TColour::sf_embedded_annotations].set_source_rgba( cr);
+ cairo_rectangle( cr, wa, 0, ww, da_ht);
+ cairo_fill( cr);
+ cairo_stroke( cr);
+
+ cairo_set_source_rgb( cr, 0., 0., 0.);
+ cairo_move_to( cr, wa, da_ht - 12 - disp);
+ cairo_show_text( cr, A.label.c_str());
+ cairo_stroke( cr);
+ }
}
}
case TMode::showing_remixed:
--
Sleep experiment manager
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit d1e5e194cc8311eae9f02e9c051060c739c443fe
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 30 01:58:12 2013 +0300
correctly report SChannel::name()
diff --git a/src/libsigfile/channel.hh b/src/libsigfile/channel.hh
index e34281e..d8f8482 100644
--- a/src/libsigfile/channel.hh
+++ b/src/libsigfile/channel.hh
@@ -145,14 +145,17 @@ struct SChannel {
const char* name() const
{
- switch ( _type ) {
- case TType::eeg: return channel_sTType::eeg( _idx);
- case TType::eog: return channel_sTType::eog( _idx);
- case TType::emg: return channel_sTType::emg( _idx);
- case TType::ecg: return channel_sTType::ecg( _idx);
- case TType::erg: return channel_sTType::erg( _idx);
- default: return _custom_name.c_str();
- }
+ if ( _custom_name.empty() )
+ switch ( _type ) {
+ case TType::eeg: return channel_sTType::eeg(
_idx);
+ case TType::eog: return channel_sTType::eog(
_idx);
+ case TType::emg: return channel_sTType::emg(
_idx);
+ case TType::ecg: return channel_sTType::ecg(
_idx);
+ case TType::erg: return channel_sTType::erg(
_idx);
+ default: return (unknown);
+ }
+ else
+ return _custom_name.c_str();
}
const char* c_str() const
{ return name(); }
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit d13ebbb3e0639d605eb883401a32b2066b0e8309 Author: Andrei Zavada johnhom...@gmail.com Date: Thu Apr 25 02:18:51 2013 +0300 glade ambivalence towards use_action_appearance diff --git a/data/mw-dialogs.glade b/data/mw-dialogs.glade index 01db660..8d5fe47 100644 --- a/data/mw-dialogs.glade +++ b/data/mw-dialogs.glade @@ -293,11 +293,9 @@ child object class=GtkButton id=button2 property name=label_Dismiss/property -property name=use_action_appearanceFalse/property property name=visibleTrue/property property name=can_focusTrue/property property name=receives_defaultTrue/property -property name=use_action_appearanceFalse/property property name=use_underlineTrue/property /object packing @@ -864,11 +862,9 @@ With bug reports, either send yours to lt;a href=mailto:aghermann-users@lists. child object class=GtkButton id=button1 property name=labelgtk-cancel/property -property name=use_action_appearanceFalse/property property name=visibleTrue/property property name=can_focusTrue/property property name=receives_defaultTrue/property -property name=use_action_appearanceFalse/property property name=use_stockTrue/property /object packing @@ -880,13 +876,11 @@ With bug reports, either send yours to lt;a href=mailto:aghermann-users@lists. child object class=GtkButton id=bBatchRunExecute property name=labelgtk-execute/property -property name=use_action_appearanceFalse/property property name=visibleTrue/property property name=can_focusTrue/property property name=can_defaultTrue/property property name=has_defaultTrue/property property name=receives_defaultTrue/property -property name=use_action_appearanceFalse/property property name=use_stockTrue/property /object packing @@ -939,12 +933,10 @@ With bug reports, either send yours to lt;a href=mailto:aghermann-users@lists. child object class=GtkButton id=bEDFFileDetailsDismiss property name=label_Dismiss/property -property name=use_action_appearanceFalse/property property name=visibleTrue/property property name=can_focusTrue/property property name=is_focusTrue/property property name=receives_defaultTrue/property -property name=use_action_appearanceFalse/property property name=reliefhalf/property property name=use_underlineTrue/property /object @@ -1052,10 +1044,8 @@ With bug reports, either send yours to lt;a href=mailto:aghermann-users@lists. child object class=GtkButton id=bEdfImportEdfhed property name=label translatable=yesView/_Score separately/property -property name=use_action_appearanceFalse/property property name=can_focusTrue/property property name=receives_defaultTrue/property -property name=use_action_appearanceFalse/property property name=reliefnone/property property name=use_underlineTrue/property /object @@ -1068,11 +1058,9 @@ With bug reports, either send yours to lt;a href=mailto:aghermann-users@lists. child object class=GtkButton id=bEdfImportDrop property name=label translatable=yes_Drop/property -property name=use_action_appearanceFalse/property property name=visibleTrue/property property name=can_focusFalse/property property name=receives_defaultTrue/property -property name=use_action_appearanceFalse/property property name=reliefhalf/property property name=use_underlineTrue/property /object @@ -1085,13 +1073,11 @@ With bug reports, either send yours to lt;a href=mailto:aghermann-users@lists. child object class=GtkButton id=bEdfImportAdmit property name=label translatable=yes_Admit/property -property name=use_action_appearanceFalse/property property name=visibleTrue/property property name=can_focusFalse/property property name=can_defaultTrue/property property name=has_defaultTrue/property property name=receives_defaultTrue/property -property
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 8517e15ee8a5dd1b0e43044f1280b9c41f5885a1
Author: Andrei Zavada johnhom...@gmail.com
Date: Fri Apr 26 00:26:42 2013 +0300
mention embedded annotations in global annotations dialog
diff --git a/src/expdesign/primaries.cc b/src/expdesign/primaries.cc
index c5e478f..695a110 100644
--- a/src/expdesign/primaries.cc
+++ b/src/expdesign/primaries.cc
@@ -448,6 +448,8 @@ get_annotations() const
for ( auto A : AA )
ret.emplace_back( F(), h, A);
}
+ for ( auto A : F().annotations() )
+ ret.emplace_back( F(), -1, A);
}
ret.sort();
return ret;
diff --git a/src/expdesign/primaries.hh b/src/expdesign/primaries.hh
index 12861c9..0e18d99 100644
--- a/src/expdesign/primaries.hh
+++ b/src/expdesign/primaries.hh
@@ -154,9 +154,9 @@ class CSubject : public SSubjectId {
}
const char*
- channel()
+ channel() const
{
- return _source.channel_by_id(_h);
+ return (_h == -1) ? (embedded) :
_source.channel_by_id(_h);
}
agh::alg::SSpanfloat
page_span( size_t pagesize) const
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit a010d93338c171a3e8673aae4e890f7474e29a28
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 30 14:36:05 2013 +0300
more relaxed treatment of maxmin conditions
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index 2edd205..d1f7f5d 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -785,14 +785,11 @@ _parse_header()
for ( auto H : channels )
if ( H.ucd.type() !=
sigfile::SChannel::TType::embedded_annotation ) {
if ( H.physical_max = H.physical_min ||
-H.digital_max = H.digital_min ) {
+H.digital_max = H.digital_min )
_status |= nogain;
- if ( not (flags() no_field_consistency_check)
)
- return -2;
- } else
- H.scale =
- (H.physical_max - H.physical_min) /
- (H.digital_max - H.digital_min );
+ H.scale =
+ (H.physical_max - H.physical_min) /
+ (H.digital_max - H.digital_min );
}
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 4ebefa7399094351022ce647b1e3a284b18c4d19
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 23 18:32:11 2013 +0300
fix OMP-assisted crash when taking FFT on channels wth variable samplerates
diff --git a/ChangeLog b/ChangeLog
index 776304a..3f57c94 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -9,6 +9,8 @@ v.0.9 (2013-xx-xx)
* Make all timestamps in sidecar files (a) relative to recording
start, (b) expressed in seconds, to be consistent with embedded
annotations.
+ * Fix crash when getting PSD on montage having channels with
+ variable sample rate, on OMP-enabled hosts.
v.0.8.2 (2013-04-07)
* Fix GtkScrolledWindow issue in Annotations dialog.
diff --git a/src/metrics/psd.cc b/src/metrics/psd.cc
index dbb7faf..50cc355 100644
--- a/src/metrics/psd.cc
+++ b/src/metrics/psd.cc
@@ -161,8 +161,7 @@ go_compute()
valarraydouble// buffer for PSD
P (spp+2);
- static fftw_plan fft_plan = NULL;
- static size_t saved_spp = 0;
+ static mapsize_t, fftw_plan plannen;
#ifdef _OPENMP
#pragma omp critical
#endif
@@ -177,13 +176,12 @@ go_compute()
//#endif
// }
// use single-threaded fftw; SMP active at a higher level
- if ( fft_plan == nullptr || spp != saved_spp ) {
+ if ( plannen.find( spp) == plannen.end() ) {
printf( Preparing fftw plan for %zu samples..., spp);
- saved_spp = spp;
- memcpy( fft_Ti, S[0], spp * sizeof(double)); // not
necessary?
- fft_plan = fftw_plan_dft_r2c_1d(
+ //memcpy( fft_Ti, S[0], spp * sizeof(double)); // not
necessary?
+ plannen[spp] = fftw_plan_dft_r2c_1d(
spp, fft_Ti, (fftw_complex*)fft_To,
plan_flags(Pp.plan_type));
printf( done\n);
@@ -214,7 +212,7 @@ go_compute()
for ( size_t s = 0; s spp; ++s )
fft_Ti[s] *= W[s];
- fftw_execute_dft_r2c( fft_plan, fft_Ti, (fftw_complex*)fft_To);
+ fftw_execute_dft_r2c( plannen[spp], fft_Ti,
(fftw_complex*)fft_To);
// thanks http://www.fftw.org/fftw2_doc/fftw_2.html
P[0] = fft_To[0] * fft_To[0]; /* DC component */
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit a12e2683a8b2290d759c67ea4a8ac7c440eeded8
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 23 13:54:59 2013 +0300
tweak DnD code to accept edf+c files, tell user of any problems
diff --git a/src/ui/mw/admit-one.cc b/src/ui/mw/admit-one.cc
index 1ffcafa..5242935 100644
--- a/src/ui/mw/admit-one.cc
+++ b/src/ui/mw/admit-one.cc
@@ -28,19 +28,43 @@ dnd_maybe_admit_one( const char* fname)
string info;
try {
Fp = new CTypedSource (fname, ED-fft_params.pagesize);
- if ( Fp-type() == CTypedSource::TType::edf (*Fp)().status()
CEDFFile::TStatus::inoperable ) {
- pop_ok_message( wMainWindow, Bad EDF file, The file
i%s/i doesn't appear to be a valid EDF file, fname);
+ switch ( Fp-type() ) {
+ case CTypedSource::TType::edf:
+ case CTypedSource::TType::edfplus:
+ {
+ CEDFFile F = *static_castCEDFFile* ((*Fp)());
+ if ( F.subtype() == CEDFFile::TSubtype::edfplus_d ) {
+ pop_ok_message(
+ wMainWindow, EDF+D Unsupported, The
file b%s/b is in EDF+D format, which is not supported yet,
+ fname);
+ return 0;
+ }
+ if ( F.status() CEDFFile::TStatus::inoperable ) {
+ pop_ok_message(
+ wMainWindow, Bad EDF file, The file
b%s/b cannot be processed due to these issues:\n\n%s,
+ fname, F.explain_status().c_str());
+ return 0;
+ }
+
+ info = (*Fp)().details(
0|sigfile::CEDFFile::with_channels);
+ gtk_label_set_markup(
+ lEdfImportCaption,
+ (snprintf_buf( File: i%s/i, fname),
+__buf__));
+ gtk_label_set_markup(
+ lEdfImportSubject,
+ (snprintf_buf( b%s/b (%s),
F.subject().id.c_str(), F.subject().name.c_str()),
+__buf__));
+ }
+ break;
+ default:
+ pop_ok_message( wMainWindow, Unsupported format, The
file b%s/b is in unrecognised format. Sorry., fname);
return 0;
}
- info = (*Fp)().details( 0|sigfile::CEDFFile::with_channels);
-
- snprintf_buf( File: i%s/i, fname);
- gtk_label_set_markup( lEdfImportCaption, __buf__);
- snprintf_buf( b%s/b (%s), (*Fp)().subject().id.c_str(),
(*Fp)().subject().name.c_str());
- gtk_label_set_markup( lEdfImportSubject, __buf__);
} catch ( exception ex) {
- pop_ok_message( wMainWindow, Bad EDF , File i%s/i
doesn't appear to be a valid EDF file, fname);
+ pop_ok_message( wMainWindow, Corrupted EDF file, File
b%s/b doesn't appear to have a valid header:\n\n%s,
+ fname, (*Fp)().explain_status().c_str());
return 0;
}
gtk_text_buffer_set_text( tEDFFileDetailsReport, info.c_str(), -1);
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 7b96fc5abbacdaf7e9f18b74646bfbee532caf8f
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 23 16:40:01 2013 +0300
shorter break out of nested cycle when checking for channel uniqueness
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index eb8002e..57b9a8d 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -816,11 +816,14 @@ _parse_header()
// are channels unique?
for ( auto H : channels )
- for ( auto J : channels )
+ for ( auto J : channels ) {
if ( J != H J.label == H.label ) {
_status |= dup_channels;
- break;
+ goto outer_break;
}
+ }
+outer_break:
+
return 0;
}
--
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit a6da6dd223d35f90f2bfd1cfcde37cba21bc638c
Author: Andrei Zavada johnhom...@gmail.com
Date: Tue Apr 23 00:59:53 2013 +0300
properly do afd290475
diff --git a/src/ui/mw/measurements_cb.cc b/src/ui/mw/measurements_cb.cc
index 7470f16..fc7be3d 100644
--- a/src/ui/mw/measurements_cb.cc
+++ b/src/ui/mw/measurements_cb.cc
@@ -127,7 +127,8 @@ daSubjectTimeline_scroll_event_cb(
auto J = *(SExpDesignUI::SSubjectPresentation*)userdata;
auto ED = J._p._p;
- if ( event-state (GDK_CONTROL_MASK | GDK_SHIFT_MASK) ) {
+ if ( event-state GDK_CONTROL_MASK
+event-state GDK_SHIFT_MASK ) {
ED.modify_profile_scales( event-direction);
gtk_widget_queue_draw( (GtkWidget*)ED.cMeasurements);
return TRUE;
--
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[med-svn] r13447 - trunk/packages/R/r-cran-genetics/trunk/debian
Author: plessy Date: 2013-05-01 00:21:58 + (Wed, 01 May 2013) New Revision: 13447 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog trunk/packages/R/r-cran-genetics/trunk/debian/copyright Log: New upstream release ; no new copyright nor license notice. Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog === --- trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-04-30 20:28:23 UTC (rev 13446) +++ trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:21:58 UTC (rev 13447) @@ -1,3 +1,9 @@ +r-cran-genetics (1.3.8-1) UNRELEASED; urgency=low + + * New upstream release. + + -- Charles Plessy ple...@debian.org Mon, 29 Apr 2013 18:38:47 +0900 + r-cran-genetics (1.3.6-2) unstable; urgency=low * debian/control: Modified: trunk/packages/R/r-cran-genetics/trunk/debian/copyright === --- trunk/packages/R/r-cran-genetics/trunk/debian/copyright 2013-04-30 20:28:23 UTC (rev 13446) +++ trunk/packages/R/r-cran-genetics/trunk/debian/copyright 2013-05-01 00:21:58 UTC (rev 13447) @@ -1,5 +1,5 @@ Format: http://dep.debian.net/deps/dep5/ -Source: http://cran.r-project.org/src/contrib/genetics_1.3.6.tar.gz +Source: http://cran.r-project.org/src/contrib/genetics_1.3.8.tar.gz Files: * Copyright : Genetics is copyright 2003-2008 of Gregory Warnes war...@bst.rochester.edu, ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13448 - trunk/packages/R/r-cran-genetics/trunk/debian
Author: plessy Date: 2013-05-01 00:31:55 + (Wed, 01 May 2013) New Revision: 13448 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog trunk/packages/R/r-cran-genetics/trunk/debian/control Log: Normalised VCS URLs following Lintian's standard. Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog === --- trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:21:58 UTC (rev 13447) +++ trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:31:55 UTC (rev 13448) @@ -1,6 +1,7 @@ r-cran-genetics (1.3.8-1) UNRELEASED; urgency=low * New upstream release. + * Normalised VCS URLs following Lintian's standard. -- Charles Plessy ple...@debian.org Mon, 29 Apr 2013 18:38:47 +0900 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/control === --- trunk/packages/R/r-cran-genetics/trunk/debian/control 2013-05-01 00:21:58 UTC (rev 13447) +++ trunk/packages/R/r-cran-genetics/trunk/debian/control 2013-05-01 00:31:55 UTC (rev 13448) @@ -8,8 +8,8 @@ Andreas Tille ti...@debian.org Build-Depends: debhelper (= 8), cdbs, r-base-dev, r-cran-combinat, r-cran-mvtnorm, r-cran-gdata, r-cran-gtools, r-cran-mass Standards-Version: 3.9.2 -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-genetics/trunk/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-cran-genetics/trunk/ +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-genetics/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-genetics/trunk/ Homepage: http://cran.r-project.org/web/packages/genetics Package: r-cran-genetics ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13449 - trunk/packages/R/r-cran-genetics/trunk/debian
Author: plessy Date: 2013-05-01 00:32:27 + (Wed, 01 May 2013) New Revision: 13449 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog trunk/packages/R/r-cran-genetics/trunk/debian/control Log: Removed obsolete DM-Upload-Allowed field. Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog === --- trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:31:55 UTC (rev 13448) +++ trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:32:27 UTC (rev 13449) @@ -2,6 +2,7 @@ * New upstream release. * Normalised VCS URLs following Lintian's standard. + * Removed obsolete DM-Upload-Allowed field. -- Charles Plessy ple...@debian.org Mon, 29 Apr 2013 18:38:47 +0900 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/control === --- trunk/packages/R/r-cran-genetics/trunk/debian/control 2013-05-01 00:31:55 UTC (rev 13448) +++ trunk/packages/R/r-cran-genetics/trunk/debian/control 2013-05-01 00:32:27 UTC (rev 13449) @@ -2,7 +2,6 @@ Section: gnu-r Priority: optional Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org -DM-Upload-Allowed: yes Uploaders: Steffen Moeller moel...@debian.org, Charles Plessy ple...@debian.org, Andreas Tille ti...@debian.org ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13450 - trunk/packages/R/r-cran-genetics/trunk/debian
Author: plessy Date: 2013-05-01 00:33:02 + (Wed, 01 May 2013) New Revision: 13450 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog trunk/packages/R/r-cran-genetics/trunk/debian/compat trunk/packages/R/r-cran-genetics/trunk/debian/control Log: Using Debhelper 9. Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog === --- trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:32:27 UTC (rev 13449) +++ trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:33:02 UTC (rev 13450) @@ -3,6 +3,7 @@ * New upstream release. * Normalised VCS URLs following Lintian's standard. * Removed obsolete DM-Upload-Allowed field. + * Using Debhelper 9. -- Charles Plessy ple...@debian.org Mon, 29 Apr 2013 18:38:47 +0900 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/compat === --- trunk/packages/R/r-cran-genetics/trunk/debian/compat2013-05-01 00:32:27 UTC (rev 13449) +++ trunk/packages/R/r-cran-genetics/trunk/debian/compat2013-05-01 00:33:02 UTC (rev 13450) @@ -1 +1 @@ -8 +9 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/control === --- trunk/packages/R/r-cran-genetics/trunk/debian/control 2013-05-01 00:32:27 UTC (rev 13449) +++ trunk/packages/R/r-cran-genetics/trunk/debian/control 2013-05-01 00:33:02 UTC (rev 13450) @@ -5,7 +5,7 @@ Uploaders: Steffen Moeller moel...@debian.org, Charles Plessy ple...@debian.org, Andreas Tille ti...@debian.org -Build-Depends: debhelper (= 8), cdbs, r-base-dev, r-cran-combinat, r-cran-mvtnorm, r-cran-gdata, r-cran-gtools, r-cran-mass +Build-Depends: debhelper (= 9), cdbs, r-base-dev, r-cran-combinat, r-cran-mvtnorm, r-cran-gdata, r-cran-gtools, r-cran-mass Standards-Version: 3.9.2 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-genetics/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-genetics/trunk/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13451 - trunk/packages/R/r-cran-genetics/trunk/debian
Author: plessy Date: 2013-05-01 00:33:26 + (Wed, 01 May 2013) New Revision: 13451 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/rules Log: Removed copyright notice for this trivial file. Modified: trunk/packages/R/r-cran-genetics/trunk/debian/rules === --- trunk/packages/R/r-cran-genetics/trunk/debian/rules 2013-05-01 00:33:02 UTC (rev 13450) +++ trunk/packages/R/r-cran-genetics/trunk/debian/rules 2013-05-01 00:33:26 UTC (rev 13451) @@ -1,7 +1,4 @@ #!/usr/bin/make -f -# -*- makefile -*- -# debian/rules file for the Debian/GNU Linux r-cran-genetics package -# Copyright 2008 by Steffen Moeller moel...@debian.org include /usr/share/R/debian/r-cran.mk ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13452 - trunk/packages/R/r-cran-genetics/trunk/debian
Author: plessy Date: 2013-05-01 00:34:02 + (Wed, 01 May 2013) New Revision: 13452 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog trunk/packages/R/r-cran-genetics/trunk/debian/rules Log: Acquire R:Depends directly from r-base-dev. Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog === --- trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:33:26 UTC (rev 13451) +++ trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:34:02 UTC (rev 13452) @@ -4,6 +4,7 @@ * Normalised VCS URLs following Lintian's standard. * Removed obsolete DM-Upload-Allowed field. * Using Debhelper 9. + * Acquire R:Depends directly from r-base-dev. -- Charles Plessy ple...@debian.org Mon, 29 Apr 2013 18:38:47 +0900 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/rules === --- trunk/packages/R/r-cran-genetics/trunk/debian/rules 2013-05-01 00:33:26 UTC (rev 13451) +++ trunk/packages/R/r-cran-genetics/trunk/debian/rules 2013-05-01 00:34:02 UTC (rev 13452) @@ -2,7 +2,5 @@ include /usr/share/R/debian/r-cran.mk -# Require a number equal or superior than the R version the package was built with. install/$(package):: - echo R:Depends=r-base-core (= $(shell R --version | head -n1 | perl -ne 'print / +([0-9]\.[0-9]+\.[0-9])/')~) debian/$(package).substvars chmod 644 debian/$(package)/usr/lib/R/site-library/genetics/doc/*.pdf ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13453 - trunk/packages/R/r-cran-genetics/trunk/debian
Author: plessy
Date: 2013-05-01 00:35:28 + (Wed, 01 May 2013)
New Revision: 13453
Modified:
trunk/packages/R/r-cran-genetics/trunk/debian/changelog
trunk/packages/R/r-cran-genetics/trunk/debian/control
trunk/packages/R/r-cran-genetics/trunk/debian/copyright
Log:
Normalised VCS URLs following Lintian's standard.
Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog
===
--- trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01
00:34:02 UTC (rev 13452)
+++ trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01
00:35:28 UTC (rev 13453)
@@ -5,6 +5,7 @@
* Removed obsolete DM-Upload-Allowed field.
* Using Debhelper 9.
* Acquire R:Depends directly from r-base-dev.
+ * Normalised VCS URLs following Lintian's standard.
-- Charles Plessy ple...@debian.org Mon, 29 Apr 2013 18:38:47 +0900
Modified: trunk/packages/R/r-cran-genetics/trunk/debian/control
===
--- trunk/packages/R/r-cran-genetics/trunk/debian/control 2013-05-01
00:34:02 UTC (rev 13452)
+++ trunk/packages/R/r-cran-genetics/trunk/debian/control 2013-05-01
00:35:28 UTC (rev 13453)
@@ -1,11 +1,18 @@
Source: r-cran-genetics
-Section: gnu-r
-Priority: optional
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
Uploaders: Steffen Moeller moel...@debian.org,
Charles Plessy ple...@debian.org,
Andreas Tille ti...@debian.org
-Build-Depends: debhelper (= 9), cdbs, r-base-dev, r-cran-combinat,
r-cran-mvtnorm, r-cran-gdata, r-cran-gtools, r-cran-mass
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (= 9),
+ cdbs,
+ r-base-dev,
+ r-cran-combinat,
+ r-cran-mvtnorm,
+ r-cran-gdata,
+ r-cran-gtools,
+ r-cran-mass
Standards-Version: 3.9.2
Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-genetics/trunk/
Vcs-Svn:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-genetics/trunk/
@@ -13,7 +20,14 @@
Package: r-cran-genetics
Architecture: all
-Depends: ${R:Depends}, ${misc:Depends}, r-recommended, r-cran-gtools,
r-cran-gdata, r-cran-combinat, r-cran-mvtnorm, r-cran-mass
+Depends: ${R:Depends},
+ ${misc:Depends},
+ r-recommended,
+ r-cran-gtools,
+ r-cran-gdata,
+ r-cran-combinat,
+ r-cran-mvtnorm,
+ r-cran-mass
Description: GNU R package for population genetics
Classes and methods for handling genetic data. Includes
The package provides a library for the statistics environment R that
@@ -29,3 +43,4 @@
The R-Genetics project has developed an set of enhanced genetics
packages to replace 'genetics'. Please visit the project homepage
at http://rgenetics.org for information.
+
Modified: trunk/packages/R/r-cran-genetics/trunk/debian/copyright
===
--- trunk/packages/R/r-cran-genetics/trunk/debian/copyright 2013-05-01
00:34:02 UTC (rev 13452)
+++ trunk/packages/R/r-cran-genetics/trunk/debian/copyright 2013-05-01
00:35:28 UTC (rev 13453)
@@ -1,8 +1,8 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: http://cran.r-project.org/src/contrib/genetics_1.3.8.tar.gz
Files: *
-Copyright : Genetics is copyright 2003-2008 of Gregory Warnes
war...@bst.rochester.edu,
+Copyright: Genetics is copyright 2003-2008 of Gregory Warnes
war...@bst.rochester.edu,
with contributions from David Duffy dav...@qumr.edu.au,
Gregor Gorjanc,
Friedrich Leisch,
@@ -46,3 +46,4 @@
This package was created by Steffen Moeller moel...@debian.org,
based on work for the r-cran-rodbc package of Dirk
Eddelbuettel e...@debian.org.
+
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[med-svn] r13454 - trunk/packages/R/r-cran-genetics/trunk/debian
Author: plessy Date: 2013-05-01 00:36:19 + (Wed, 01 May 2013) New Revision: 13454 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog trunk/packages/R/r-cran-genetics/trunk/debian/control Log: Conforms with Policy 3.9.4. Modified: trunk/packages/R/r-cran-genetics/trunk/debian/changelog === --- trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:35:28 UTC (rev 13453) +++ trunk/packages/R/r-cran-genetics/trunk/debian/changelog 2013-05-01 00:36:19 UTC (rev 13454) @@ -6,6 +6,7 @@ * Using Debhelper 9. * Acquire R:Depends directly from r-base-dev. * Normalised VCS URLs following Lintian's standard. + * Conforms with Policy 3.9.4. -- Charles Plessy ple...@debian.org Mon, 29 Apr 2013 18:38:47 +0900 Modified: trunk/packages/R/r-cran-genetics/trunk/debian/control === --- trunk/packages/R/r-cran-genetics/trunk/debian/control 2013-05-01 00:35:28 UTC (rev 13453) +++ trunk/packages/R/r-cran-genetics/trunk/debian/control 2013-05-01 00:36:19 UTC (rev 13454) @@ -13,7 +13,7 @@ r-cran-gdata, r-cran-gtools, r-cran-mass -Standards-Version: 3.9.2 +Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-genetics/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-genetics/trunk/ Homepage: http://cran.r-project.org/web/packages/genetics ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit f0718bd742b1663204ee9675df45102438bb5293
Author: Andrei Zavada johnhom...@gmail.com
Date: Thu Apr 25 15:29:03 2013 +0300
lessen templatedness of make_fname_* functions
diff --git a/src/libsigfile/source-base.hh b/src/libsigfile/source-base.hh
index 4a3ce2b..9357e89 100644
--- a/src/libsigfile/source-base.hh
+++ b/src/libsigfile/source-base.hh
@@ -27,33 +27,29 @@ using namespace std;
namespace sigfile {
-templateclass T
-string
-make_fname_hypnogram( const T _filename, size_t pagesize)
+inline string
+make_fname_hypnogram( const string _filename, size_t pagesize)
{
return agh::fs::make_fname_base( _filename, .edf, true)
+ - + to_string( (long long unsigned)pagesize) + .hypnogram;
}
-templateclass T
-string
-make_fname_artifacts( const T _filename, const SChannel channel)
+inline string
+make_fname_artifacts( const string _filename, const SChannel channel)
{
return agh::fs::make_fname_base( _filename, .edf, true)
+ - + channel + .af;
}
-templateclass T
-string
-make_fname_annotations( const T _filename, const SChannel channel)
+inline string
+make_fname_annotations( const string _filename, const SChannel channel)
{
return agh::fs::make_fname_base( _filename, .edf, true)
+ - + channel + .annotations;
}
-templateclass T
-string
-make_fname_filters( const T _filename)
+inline string
+make_fname_filters( const string _filename)
{
return agh::fs::make_fname_base( _filename, .edf, true)
+ .filters;
--
Sleep experiment manager
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit f266f70263cdcea44fd0cf12548015075e79c98a
Author: Andrei Zavada johnhom...@gmail.com
Date: Sat Apr 27 12:57:57 2013 +0300
separate sf_cb.hh from sf.hh
diff --git a/src/ui/sf/Makefile.am b/src/ui/sf/Makefile.am
index 4e40167..298c6e8 100644
--- a/src/ui/sf/Makefile.am
+++ b/src/ui/sf/Makefile.am
@@ -23,11 +23,13 @@ liba_a_SOURCES := \
widgets.hh \
sf.cc \
sf.hh \
+ sf_cb.hh \
sf_cb.cc
if DO_PCH
BUILT_SOURCES = \
sf.hh.gch \
+ sf_cb.hh.gch \
widgets.hh.gch
%.hh.gch: %.hh
$(CXXCOMPILE) -c $
diff --git a/src/ui/sf/construct.cc b/src/ui/sf/construct.cc
index 0480df3..1f61201 100644
--- a/src/ui/sf/construct.cc
+++ b/src/ui/sf/construct.cc
@@ -15,6 +15,7 @@
#include ui/mw/mw.hh
#include ui/ui.hh
#include sf.hh
+#include sf_cb.hh
using namespace std;
diff --git a/src/ui/sf/ica.cc b/src/ui/sf/ica.cc
index c473cbb..8fc87a6 100644
--- a/src/ui/sf/ica.cc
+++ b/src/ui/sf/ica.cc
@@ -15,6 +15,7 @@
#include ica/ica.hh
#include ui/misc.hh
#include sf.hh
+#include sf_cb.hh
using namespace std;
diff --git a/src/ui/sf/montage_cb.cc b/src/ui/sf/montage_cb.cc
index 83da511..feedada 100644
--- a/src/ui/sf/montage_cb.cc
+++ b/src/ui/sf/montage_cb.cc
@@ -14,6 +14,7 @@
#include ui/misc.hh
#include sf.hh
+#include sf_cb.hh
#include d/artifacts.hh
#include d/artifacts-simple.hh
#include d/filters.hh
diff --git a/src/ui/sf/sf.cc b/src/ui/sf/sf.cc
index fe2a7af..b08d5fc 100644
--- a/src/ui/sf/sf.cc
+++ b/src/ui/sf/sf.cc
@@ -15,6 +15,7 @@
#include common/fs.hh
#include ui/misc.hh
#include sf.hh
+#include sf_cb.hh
#include d/artifacts.hh
#include d/filters.hh
#include d/phasediff.hh
diff --git a/src/ui/sf/sf.hh b/src/ui/sf/sf.hh
index 608b811..80256d5 100644
--- a/src/ui/sf/sf.hh
+++ b/src/ui/sf/sf.hh
@@ -9,8 +9,8 @@
* License: GPL
*/
-#ifndef _AGH_UI_SCORING_FACILITY_H
-#define _AGH_UI_SCORING_FACILITY_H
+#ifndef _AGH_UI_SF_H
+#define _AGH_UI_SF_H
#include map
#include list
@@ -756,136 +756,6 @@ channel_y0( const T h) const
} // namespace aghui
-extern C {
-
-//gboolean wScoringFacility_configure_event_cb( GtkWidget*,
GdkEventConfigure*, gpointer);
-gboolean daSFMontage_configure_event_cb( GtkWidget*, GdkEventConfigure*,
gpointer);
-
-gboolean daSFMontage_draw_cb( GtkWidget*, cairo_t*, gpointer);
-gboolean daSFMontage_button_press_event_cb( GtkWidget*, GdkEventButton*,
gpointer);
-gboolean daSFMontage_button_release_event_cb( GtkWidget*, GdkEventButton*,
gpointer);
-gboolean daSFMontage_motion_notify_event_cb( GtkWidget*, GdkEventMotion*,
gpointer);
-gboolean daSFMontage_leave_notify_event_cb( GtkWidget*, GdkEventMotion*,
gpointer);
-gboolean daSFMontage_scroll_event_cb( GtkWidget*, GdkEventScroll*, gpointer);
-
-void eSFPageSize_changed_cb( GtkComboBox*, gpointer);
-void eSFCurrentPage_value_changed_cb( GtkSpinButton*, gpointer);
-
-void bSFScoreClear_clicked_cb( GtkButton*, gpointer);
-void bSFScoreNREM1_clicked_cb( GtkButton*, gpointer);
-void bSFScoreNREM2_clicked_cb( GtkButton*, gpointer);
-void bSFScoreNREM3_clicked_cb( GtkButton*, gpointer);
-void bSFScoreNREM4_clicked_cb( GtkButton*, gpointer);
-void bSFScoreREM_clicked_cb ( GtkButton*, gpointer);
-void bSFScoreWake_clicked_cb ( GtkButton*, gpointer);
-
-void eSFCurrentPos_clicked_cb( GtkButton*, gpointer);
-void bSFForward_clicked_cb( GtkButton*, gpointer);
-void bSFBack_clicked_cb( GtkButton*, gpointer);
-void bSFGotoPrevUnscored_clicked_cb( GtkButton*, gpointer);
-void bSFGotoNextUnscored_clicked_cb( GtkButton*, gpointer);
-void bSFGotoPrevArtifact_clicked_cb( GtkButton*, gpointer);
-void bSFGotoNextArtifact_clicked_cb( GtkButton*, gpointer);
-void bSFDrawCrosshair_toggled_cb( GtkToggleButton*, gpointer);
-void bSFShowFindDialog_toggled_cb( GtkToggleButton*, gpointer);
-void bSFShowPhaseDiffDialog_toggled_cb( GtkToggleButton*, gpointer);
-void bSFRunICA_clicked_cb( GtkButton*, gpointer);
-//void bSFResetMontage_clicked_cb( GtkButton*, gpointer);
-
-
-void eSFICARemixMode_changed_cb( GtkComboBox*, gpointer);
-void eSFICANonlinearity_changed_cb( GtkComboBox*, gpointer);
-void eSFICAApproach_changed_cb( GtkComboBox*, gpointer);
-void eSFICAFineTune_toggled_cb( GtkCheckButton*, gpointer);
-void eSFICAStabilizationMode_toggled_cb( GtkCheckButton*, gpointer);
-void eSFICAa1_value_changed_cb( GtkSpinButton*, gpointer);
-void eSFICAa2_value_changed_cb( GtkSpinButton*, gpointer);
-void eSFICAmu_value_changed_cb( GtkSpinButton*, gpointer);
-void eSFICAepsilon_value_changed_cb( GtkSpinButton*, gpointer);
-void eSFICASampleSizePercent_value_changed_cb( GtkSpinButton*, gpointer);
-void eSFICANofICs_value_changed_cb( GtkSpinButton*, gpointer);
-void eSFICAEigVecFirst_value_changed_cb( GtkSpinButton*, gpointer);
-void eSFICAEigVecLast_value_changed_cb( GtkSpinButton*, gpointer);
-void eSFICAMaxIterations_value_changed_cb( GtkSpinButton*, gpointer);
-void bSFICATry_clicked_cb(
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit 218cebd35ab82b444f0ed8b96c01726aab715f62 Author: Andrei Zavada johnhom...@gmail.com Date: Sat Apr 27 01:08:15 2013 +0300 eradicate separate emg_display_scale, use signal_display_scale instead diff --git a/src/ui/sf/channel.cc b/src/ui/sf/channel.cc index d463860..ae9d237 100644 --- a/src/ui/sf/channel.cc +++ b/src/ui/sf/channel.cc @@ -96,7 +96,6 @@ SChannel (agh::CRecording r, SValidatordouble( string(h)+to_string(seq) + .psd_display_scale, psd.display_scale, SValidatordouble::SVFRangeIn (DBL_MIN, INFINITY)), SValidatordouble( string(h)+to_string(seq) + .swu_display_scale, swu.display_scale, SValidatordouble::SVFRangeIn (DBL_MIN, INFINITY)), SValidatordouble( string(h)+to_string(seq) + .mc_display_scale, mc.display_scale, SValidatordouble::SVFRangeIn (DBL_MIN, INFINITY)), - SValidatordouble( string(h)+to_string(seq) + .emg_display_scale, emg_display_scale, SValidatordouble::SVFRangeIn (DBL_MIN, INFINITY)), }), marquee_start (0.), marquee_end (0.), @@ -151,7 +150,7 @@ SChannel (agh::CRecording r, // let it be so to avoid libconfig::readFile throwing exceptions psd.display_scale = mc.display_scale = swu.display_scale = - emg_display_scale = DBL_MIN; + DBL_MIN; percent_dirty = calculate_dirty_percent(); } @@ -360,12 +359,6 @@ update_profile_display_scales() swu.course, swu.course.size(), _p.interchannel_gap/2.); - - emg_display_scale = - agh::alg::calibrate_display_scale( - raw_profile, - raw_profile.size(), - _p.interchannel_gap/2.); } diff --git a/src/ui/sf/montage-overlays.cc b/src/ui/sf/montage-overlays.cc index a860701..4858143 100644 --- a/src/ui/sf/montage-overlays.cc +++ b/src/ui/sf/montage-overlays.cc @@ -309,7 +309,7 @@ draw_overlays( cairo_t* cr, aghui::cairo_draw_envelope( cr, raw_profile, 0, raw_profile.size(), - _p.da_wd, 0., pbot - EMGProfileHeight/2, emg_display_scale); + _p.da_wd, 0., pbot - EMGProfileHeight/2, signal_display_scale/2.); // half-signal scale, looks ok? cairo_stroke( cr); cairo_pattern_destroy( cp); } diff --git a/src/ui/sf/montage.cc b/src/ui/sf/montage.cc index ce882df..4dc263a 100644 --- a/src/ui/sf/montage.cc +++ b/src/ui/sf/montage.cc @@ -163,7 +163,6 @@ expand_by_factor( const double fac) H.signal_display_scale *= fac; H.psd.display_scale *= fac; H.mc.display_scale *= fac; - H.emg_display_scale *= fac; H.zeroy *= fac; } interchannel_gap *= fac; diff --git a/src/ui/sf/montage_cb.cc b/src/ui/sf/montage_cb.cc index e5109ce..83da511 100644 --- a/src/ui/sf/montage_cb.cc +++ b/src/ui/sf/montage_cb.cc @@ -421,13 +421,11 @@ daSFMontage_scroll_event_cb( Ch-psd.display_scale /= SF._p.scroll_factor; Ch-swu.display_scale /= SF._p.scroll_factor; Ch-mc.display_scale /= SF._p.scroll_factor; - Ch-emg_display_scale /= SF._p.scroll_factor; break; case GDK_SCROLL_UP: Ch-psd.display_scale *= SF._p.scroll_factor; Ch-swu.display_scale *= SF._p.scroll_factor; Ch-mc.display_scale *= SF._p.scroll_factor; - Ch-emg_display_scale *= SF._p.scroll_factor; break; case GDK_SCROLL_LEFT: if ( SF.cur_vpage() 0 ) @@ -448,7 +446,7 @@ daSFMontage_scroll_event_cb( H.swu.display_scale = Ch-swu.display_scale; } else if ( Ch-type == sigfile::SChannel::TType::emg H.type == sigfile::SChannel::TType::emg ) - H.emg_display_scale = Ch-emg_display_scale; + H.signal_display_scale = Ch-signal_display_scale; } gtk_widget_queue_draw( wid); } diff --git a/src/ui/sf/sf.cc b/src/ui/sf/sf.cc index 8cfbb63..fe2a7af 100644 --- a/src/ui/sf/sf.cc +++ b/src/ui/sf/sf.cc @@ -196,15 +196,6 @@ SScoringFacility (agh::CSubject J, h.swu.course.size(), interchannel_gap / 4);
[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch:
commit 21e170502c19e5c71f06b815ab96e83bad5db78e
Author: Andrei Zavada johnhom...@gmail.com
Date: Thu Apr 25 01:42:55 2013 +0300
complete e9e19394567d
diff --git a/src/ui/mw/measurements.cc b/src/ui/mw/measurements.cc
index 566cd3a..c1e54e0 100644
--- a/src/ui/mw/measurements.cc
+++ b/src/ui/mw/measurements.cc
@@ -305,7 +305,7 @@ void
aghui::SExpDesignUI::
modify_active_profile_scale( const GdkScrollDirection d)
{
- auto fac = (d == GDK_SCROLL_DOWN) ? 1/1.05 : 1.05;
+ auto fac = (d == GDK_SCROLL_DOWN) ? 1/scroll_factor : scroll_factor;
switch ( display_profile_type ) {
case metrics::TType::psd: profile_scale_psd *= fac; break;
case metrics::TType::swu: profile_scale_swu *= fac; break;
@@ -318,7 +318,7 @@ void
aghui::SExpDesignUI::
modify_profile_scales( const GdkScrollDirection d)
{
- auto fac = (d == GDK_SCROLL_DOWN) ? 1/1.05 : 1.05;
+ auto fac = (d == GDK_SCROLL_DOWN) ? 1/scroll_factor : scroll_factor;
profile_scale_psd *= fac;
profile_scale_swu *= fac;
profile_scale_mc *= fac;
--
Sleep experiment manager
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[med-svn] [SCM] aghermann branch, master, updated. c0bd21ca8eb529ade7e0c7aad22951a308a8dc8f
The following commit has been merged in the master branch: commit 97f7f879cfb5dfe734c6d9bad64c55c91e675e47 Author: Andrei Zavada johnhom...@gmail.com Date: Thu Apr 25 16:38:05 2013 +0300 don't lose embedded annotations in CEDFFile::CEDFFile(CEDFFile) diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc index 57b9a8d..a5244f9 100644 --- a/src/libsigfile/edf.cc +++ b/src/libsigfile/edf.cc @@ -408,6 +408,7 @@ CEDFFile (CEDFFile rv) swap( _session,rv._session); swap( channels, rv.channels); + swap( common_annotations, rv.common_annotations); header_length = rv.header_length; _fsize= rv._fsize; -- Sleep experiment manager ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13455 - trunk/packages/insighttoolkit/trunk/debian
Author: smr Date: 2013-05-01 04:06:45 + (Wed, 01 May 2013) New Revision: 13455 Modified: trunk/packages/insighttoolkit/trunk/debian/control.in Log: Incorporate recent changes to debian/control. Modified: trunk/packages/insighttoolkit/trunk/debian/control.in === --- trunk/packages/insighttoolkit/trunk/debian/control.in 2013-05-01 00:36:19 UTC (rev 13454) +++ trunk/packages/insighttoolkit/trunk/debian/control.in 2013-05-01 04:06:45 UTC (rev 13455) @@ -3,8 +3,7 @@ Section: science Priority: optional Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org -DM-Upload-Allowed: yes -Uploaders: Steve M. Robbins s...@debian.org, Mathieu Malaterre mathieu.malate...@gmail.com +Uploaders: Steve M. Robbins s...@debian.org Build-Depends: debhelper (= 9), cmake, cableswig (= 0.1.0+cvs20110226), gccxml (= 0.9.0+cvs20110723), zlib1g-dev (= 1.2.2), libpng12-dev, libtiff5-alt-dev, libvxl1-dev, ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13456 - in trunk/packages/insighttoolkit/trunk/debian: . patches
Author: smr Date: 2013-05-01 04:10:07 + (Wed, 01 May 2013) New Revision: 13456 Removed: trunk/packages/insighttoolkit/trunk/debian/patches/lsm-with-system-tiff.patch Modified: trunk/packages/insighttoolkit/trunk/debian/changelog trunk/packages/insighttoolkit/trunk/debian/patches/series trunk/packages/insighttoolkit/trunk/debian/rules Log: Update to new upstream. Modified: trunk/packages/insighttoolkit/trunk/debian/changelog === --- trunk/packages/insighttoolkit/trunk/debian/changelog2013-05-01 04:06:45 UTC (rev 13455) +++ trunk/packages/insighttoolkit/trunk/debian/changelog2013-05-01 04:10:07 UTC (rev 13456) @@ -1,3 +1,10 @@ +insighttoolkit4 (4.3.2-1) unstable; urgency=low + + * New upstream. +- patches/lsm-with-system-tiff.patch: Removed. Applied upstream. + + -- Steve M. Robbins s...@debian.org Tue, 30 Apr 2013 23:09:50 -0500 + insighttoolkit4 (4.3.1-3) UNRELEASED; urgency=low * Remove obsolete DMUA flag Deleted: trunk/packages/insighttoolkit/trunk/debian/patches/lsm-with-system-tiff.patch === --- trunk/packages/insighttoolkit/trunk/debian/patches/lsm-with-system-tiff.patch 2013-05-01 04:06:45 UTC (rev 13455) +++ trunk/packages/insighttoolkit/trunk/debian/patches/lsm-with-system-tiff.patch 2013-05-01 04:10:07 UTC (rev 13456) @@ -1,28 +0,0 @@ -Description: Cannot use itkLSMImageIOFactory when using system TIFF -Author: Paul Novotny p...@paulnovo.us -Forwarded: http://review.source.kitware.com/9798 - insighttoolkit4-4.3.1.orig/Modules/Compatibility/Deprecated/test/itkTestDriverIncludeDeprecatedIOFactories.h -+++ insighttoolkit4-4.3.1/Modules/Compatibility/Deprecated/test/itkTestDriverIncludeDeprecatedIOFactories.h -@@ -23,7 +23,10 @@ - #include itkNiftiImageIOFactory.h - #include itkGiplImageIOFactory.h - #include itkJPEGImageIOFactory.h --#include itkLSMImageIOFactory.h -+#include itk_tiff.h // ITK_USE_SYSTEM_TIFF -+#ifndef ITK_USE_SYSTEM_TIFF -+# include itkLSMImageIOFactory.h -+#endif // ITK_USE_SYSTEM_TIFF - #include itkMetaImageIOFactory.h - #include itkPNGImageIOFactory.h - #include itkNrrdImageIOFactory.h -@@ -43,7 +46,9 @@ - itk::ObjectFactoryBase::RegisterFactory( itk::PNGImageIOFactory::New() ); - itk::ObjectFactoryBase::RegisterFactory( itk::VTKImageIOFactory::New() ); - itk::ObjectFactoryBase::RegisterFactory( itk::GiplImageIOFactory::New() ); -+#ifndef ITK_USE_SYSTEM_TIFF - itk::ObjectFactoryBase::RegisterFactory( itk::LSMImageIOFactory::New() ); -+#endif // ITK_USE_SYSTEM_TIFF - itk::ObjectFactoryBase::RegisterFactory( itk::NiftiImageIOFactory::New() ); - itk::ObjectFactoryBase::RegisterFactory( itk::JPEGImageIOFactory::New() ); - itk::ObjectFactoryBase::RegisterFactory( itk::TIFFImageIOFactory::New() ); Modified: trunk/packages/insighttoolkit/trunk/debian/patches/series === --- trunk/packages/insighttoolkit/trunk/debian/patches/series 2013-05-01 04:06:45 UTC (rev 13455) +++ trunk/packages/insighttoolkit/trunk/debian/patches/series 2013-05-01 04:10:07 UTC (rev 13456) @@ -1,2 +1,2 @@ bsd-hdf5.patch -lsm-with-system-tiff.patch + Modified: trunk/packages/insighttoolkit/trunk/debian/rules === --- trunk/packages/insighttoolkit/trunk/debian/rules2013-05-01 04:06:45 UTC (rev 13455) +++ trunk/packages/insighttoolkit/trunk/debian/rules2013-05-01 04:10:07 UTC (rev 13456) @@ -2,7 +2,6 @@ VER_MAJOR = 4 VER_MINOR = 3 -VER_PATCH = 1 # TODO: turn on the following: # @@ -43,7 +42,6 @@ -DBUILD_EXAMPLES:BOOL=ON \ -DBUILD_TESTING:BOOL=ON -VER_FULL = $(VER_MAJOR).$(VER_MINOR).$(VER_PATCH) SOVERSION = $(VER_MAJOR).$(VER_MINOR) pkg_lib = libinsighttoolkit$(SOVERSION) ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13457 - trunk/packages/R/r-cran-genabel/trunk/debian
Author: plessy Date: 2013-05-01 05:41:08 + (Wed, 01 May 2013) New Revision: 13457 Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog trunk/packages/R/r-cran-genabel/trunk/debian/copyright Log: New upstream release, no new copyright nor license notice. Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog === --- trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01 04:10:07 UTC (rev 13456) +++ trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01 05:41:08 UTC (rev 13457) @@ -1,5 +1,11 @@ -r-cran-genabel (1.7-3-1) UNRELEASED; urgency=low +r-cran-genabel (1.7-4-1) UNRELEASED; urgency=low + * New upstream version + + -- Charles Plessy ple...@debian.org Wed, 01 May 2013 14:34:36 +0900 + +r-cran-genabel (1.7-3-1) unstable; urgency=low + * New upstream version * Replace debian/README.Debian by debian/README.test * DEP5 copyright Modified: trunk/packages/R/r-cran-genabel/trunk/debian/copyright === --- trunk/packages/R/r-cran-genabel/trunk/debian/copyright 2013-05-01 04:10:07 UTC (rev 13456) +++ trunk/packages/R/r-cran-genabel/trunk/debian/copyright 2013-05-01 05:41:08 UTC (rev 13457) @@ -1,5 +1,5 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Source: http://cran.r-project.org/src/contrib/GenABEL_1.7-0.tar.gz +Source: http://cran.r-project.org/src/contrib/GenABEL_1.7-4.tar.gz Files: * Copyright: GenABEL is copyright 2006-2008 of Yurii Aulchenko, Maksim Struchalin, with ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13458 - trunk/packages/R/r-cran-genabel/trunk/debian
Author: plessy
Date: 2013-05-01 05:44:39 + (Wed, 01 May 2013)
New Revision: 13458
Modified:
trunk/packages/R/r-cran-genabel/trunk/debian/changelog
trunk/packages/R/r-cran-genabel/trunk/debian/control
Log:
Updated qvalue package name (moved from CRAN to Bioconductor).
Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog
===
--- trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01
05:41:08 UTC (rev 13457)
+++ trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01
05:44:39 UTC (rev 13458)
@@ -1,6 +1,7 @@
r-cran-genabel (1.7-4-1) UNRELEASED; urgency=low
* New upstream version
+ * Updated qvalue package name (moved from CRAN to Bioconductor).
-- Charles Plessy ple...@debian.org Wed, 01 May 2013 14:34:36 +0900
Modified: trunk/packages/R/r-cran-genabel/trunk/debian/control
===
--- trunk/packages/R/r-cran-genabel/trunk/debian/control2013-05-01
05:41:08 UTC (rev 13457)
+++ trunk/packages/R/r-cran-genabel/trunk/debian/control2013-05-01
05:44:39 UTC (rev 13458)
@@ -14,7 +14,7 @@
Package: r-cran-genabel
Architecture: any
Depends: ${shlibs:Depends}, ${R:Depends}, r-cran-mass
-Suggests: r-cran-genetics, r-cran-haplo.stats, r-cran-qvalue
+Suggests: r-cran-genetics, r-cran-haplo.stats, r-bioc-qvalue
Provides: r-other-genabel
Conflicts: r-other-genabel
Replaces: r-other-genabel
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[med-svn] r13459 - trunk/packages/R/r-cran-genabel/trunk/debian
Author: plessy
Date: 2013-05-01 05:46:05 + (Wed, 01 May 2013)
New Revision: 13459
Modified:
trunk/packages/R/r-cran-genabel/trunk/debian/changelog
trunk/packages/R/r-cran-genabel/trunk/debian/control
Log:
Drop references to old name r-other-genabel.
Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog
===
--- trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01
05:44:39 UTC (rev 13458)
+++ trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01
05:46:05 UTC (rev 13459)
@@ -2,6 +2,7 @@
* New upstream version
* Updated qvalue package name (moved from CRAN to Bioconductor).
+ * Drop references to old name r-other-genabel.
-- Charles Plessy ple...@debian.org Wed, 01 May 2013 14:34:36 +0900
Modified: trunk/packages/R/r-cran-genabel/trunk/debian/control
===
--- trunk/packages/R/r-cran-genabel/trunk/debian/control2013-05-01
05:44:39 UTC (rev 13458)
+++ trunk/packages/R/r-cran-genabel/trunk/debian/control2013-05-01
05:46:05 UTC (rev 13459)
@@ -15,9 +15,6 @@
Architecture: any
Depends: ${shlibs:Depends}, ${R:Depends}, r-cran-mass
Suggests: r-cran-genetics, r-cran-haplo.stats, r-bioc-qvalue
-Provides: r-other-genabel
-Conflicts: r-other-genabel
-Replaces: r-other-genabel
Description: GNU R package for genome-wide SNP association analysis
The package offers the R library GenABEL for the hunt of genetic contributions
to a disease (or any other pheonypical trait) by so called genome-wide
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[med-svn] r13460 - trunk/packages/R/r-cran-genabel/trunk/debian
Author: plessy Date: 2013-05-01 05:47:00 + (Wed, 01 May 2013) New Revision: 13460 Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog trunk/packages/R/r-cran-genabel/trunk/debian/control Log: Drop build-dependance on package only suggested. Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog === --- trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01 05:46:05 UTC (rev 13459) +++ trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01 05:47:00 UTC (rev 13460) @@ -3,6 +3,7 @@ * New upstream version * Updated qvalue package name (moved from CRAN to Bioconductor). * Drop references to old name r-other-genabel. + * Drop build-dependance on package only suggested. -- Charles Plessy ple...@debian.org Wed, 01 May 2013 14:34:36 +0900 Modified: trunk/packages/R/r-cran-genabel/trunk/debian/control === --- trunk/packages/R/r-cran-genabel/trunk/debian/control2013-05-01 05:46:05 UTC (rev 13459) +++ trunk/packages/R/r-cran-genabel/trunk/debian/control2013-05-01 05:47:00 UTC (rev 13460) @@ -5,7 +5,7 @@ Uploaders: Steffen Moeller moel...@debian.org, Andreas Tille ti...@debian.org, Charles Plessy ple...@debian.org -Build-Depends: debhelper (= 9), cdbs, r-base-dev (= 2.10), r-cran-mass, r-cran-genetics, r-cran-haplo.stats, r-cran-qvalue +Build-Depends: debhelper (= 9), cdbs, r-base-dev (= 2.10), r-cran-mass Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-genabel/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-cran-genabel/trunk/ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13461 - trunk/packages/R/r-cran-genabel/trunk/debian
Author: plessy Date: 2013-05-01 05:49:28 + (Wed, 01 May 2013) New Revision: 13461 Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog trunk/packages/R/r-cran-genabel/trunk/debian/control Log: Normalised VCS URLs following Lintian's standard. Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog === --- trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01 05:47:00 UTC (rev 13460) +++ trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01 05:49:28 UTC (rev 13461) @@ -4,6 +4,7 @@ * Updated qvalue package name (moved from CRAN to Bioconductor). * Drop references to old name r-other-genabel. * Drop build-dependance on package only suggested. + * Normalised VCS URLs following Lintian's standard. -- Charles Plessy ple...@debian.org Wed, 01 May 2013 14:34:36 +0900 Modified: trunk/packages/R/r-cran-genabel/trunk/debian/control === --- trunk/packages/R/r-cran-genabel/trunk/debian/control2013-05-01 05:47:00 UTC (rev 13460) +++ trunk/packages/R/r-cran-genabel/trunk/debian/control2013-05-01 05:49:28 UTC (rev 13461) @@ -7,8 +7,8 @@ Charles Plessy ple...@debian.org Build-Depends: debhelper (= 9), cdbs, r-base-dev (= 2.10), r-cran-mass Standards-Version: 3.9.4 -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-genabel/trunk/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-cran-genabel/trunk/ +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-genabel/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-genabel/trunk/ Homepage: http://www.genabel.org/ Package: r-cran-genabel ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13462 - trunk/packages/R/r-cran-genabel/trunk/debian
Author: plessy Date: 2013-05-01 05:49:51 + (Wed, 01 May 2013) New Revision: 13462 Modified: trunk/packages/R/r-cran-genabel/trunk/debian/rules Log: Removed copyright notice for this trivial file. Modified: trunk/packages/R/r-cran-genabel/trunk/debian/rules === --- trunk/packages/R/r-cran-genabel/trunk/debian/rules 2013-05-01 05:49:28 UTC (rev 13461) +++ trunk/packages/R/r-cran-genabel/trunk/debian/rules 2013-05-01 05:49:51 UTC (rev 13462) @@ -1,8 +1,4 @@ #!/usr/bin/make -f -# -*- makefile -*- -# debian/rules file for the Debian/GNU Linux r-cran-genabel package -# Copyright 2008-2011 by Steffen Moeller moel...@debian.org -# 2011 by Andreas Tille ti...@debian.org debRreposname=cran include /usr/share/R/debian/r-cran.mk ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13463 - trunk/packages/R/r-cran-genabel/trunk/debian
Author: plessy
Date: 2013-05-01 05:50:30 + (Wed, 01 May 2013)
New Revision: 13463
Modified:
trunk/packages/R/r-cran-genabel/trunk/debian/changelog
trunk/packages/R/r-cran-genabel/trunk/debian/rules
Log:
Acquire R:Depends directly from r-base-dev.
Modified: trunk/packages/R/r-cran-genabel/trunk/debian/changelog
===
--- trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01
05:49:51 UTC (rev 13462)
+++ trunk/packages/R/r-cran-genabel/trunk/debian/changelog 2013-05-01
05:50:30 UTC (rev 13463)
@@ -5,6 +5,7 @@
* Drop references to old name r-other-genabel.
* Drop build-dependance on package only suggested.
* Normalised VCS URLs following Lintian's standard.
+ * Acquire R:Depends directly from r-base-dev.
-- Charles Plessy ple...@debian.org Wed, 01 May 2013 14:34:36 +0900
Modified: trunk/packages/R/r-cran-genabel/trunk/debian/rules
===
--- trunk/packages/R/r-cran-genabel/trunk/debian/rules 2013-05-01 05:49:51 UTC
(rev 13462)
+++ trunk/packages/R/r-cran-genabel/trunk/debian/rules 2013-05-01 05:50:30 UTC
(rev 13463)
@@ -4,8 +4,6 @@
include /usr/share/R/debian/r-cran.mk
install/$(package)::
- ## Require a number equal or superior than the R version the package
was built with.
- echo R:Depends=r-base-core (= $(shell R --version | head -n1 | perl
-ne 'print / +([0-9]\.[0-9]+\.[0-9])/')~) debian/$(package).substvars
find debian/$(package)/usr/lib/R/site-library/GenABEL/ -type f -exec
chmod 644 \{\} \;
DEB_INSTALL_CHANGELOGS_ALL = CHANGES.LOG
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