diff --git a/bin/name2id.m b/bin/name2id.m
index 6dfd4597e1709936474fe5dfdbbafb813e1b3b97..4c1c1798b91392b2f396d238c4d49757de124202 100644
--- a/bin/name2id.m
+++ b/bin/name2id.m
@@ -1,68 +1,71 @@
-function [species_id,from_language] = name2id(birdnames, from_language, exactfit)
- if nargin<3
- exactfit=true;
+function [species_id, from_language] = name2id(birdnames, from_language, exactfit)
+ if nargin < 3
+ exactfit = true;
end
-
+
allbird_names = evalin('base', 'allbird_names');
- if iscell(birdnames)&&numel(birdnames)==1&&~isempty(strfind(birdnames{1},'{'))
- birdnames=birdnames{1};
+ if iscell(birdnames) && numel(birdnames) == 1 && ~isempty(strfind(birdnames{1}, '{'))
+ birdnames = birdnames{1};
end
if ischar(birdnames)
- if strfind(birdnames,'{')>0
- birdnames=eval(birdnames);
+ if strfind(birdnames, '{') > 0
+ birdnames = eval(birdnames);
else
- birdnames={birdnames};
+ birdnames = {birdnames};
end
end
- supportedlang = {'species_id','Order','Family','Scientific','English','Catalan',...
- 'Chinese','Chinese_Traditional_','Croatian','Czech','Danish','Dutch',...
- 'Finnish','French','German','Italian','Japanese','Lithuanian','Norwegian',...
- 'Polish','Portuguese_Lusophone_','Portuguese_Portuguese_','Russian',...
- 'Serbian','Slovak','Spanish','Swedish','Turkish','Ukrainian','Afrikaans',...
- 'Arabic','Belarusian','Bulgarian','Estonian','French_Gaudin_','Greek',...
- 'Hebrew','Hungarian','Icelandic','Indonesian','Korean','Latvian','Macedonian',...
- 'Malayalam','NorthernSami','Persian','Romanian','Slovenian','Thai','XCname',...
- 'en_family','nl_family','family_id','BreedingRange','BreedingSubRange','NonbreedingRange'};
+ supportedlang = {'species_id', 'Order', 'Family', 'Scientific', 'English', 'Catalan', ...
+ 'Chinese', 'Chinese_Traditional_', 'Croatian', 'Czech', 'Danish', 'Dutch', ...
+ 'Finnish', 'French', 'German', 'Italian', 'Japanese', 'Lithuanian', 'Norwegian', ...
+ 'Polish', 'Portuguese_Lusophone_', 'Portuguese_Portuguese_', 'Russian', ...
+ 'Serbian', 'Slovak', 'Spanish', 'Swedish', 'Turkish', 'Ukrainian', 'Afrikaans', ...
+ 'Arabic', 'Belarusian', 'Bulgarian', 'Estonian', 'French_Gaudin_', 'Greek', ...
+ 'Hebrew', 'Hungarian', 'Icelandic', 'Indonesian', 'Korean', 'Latvian', 'Macedonian', ...
+ 'Malayalam', 'NorthernSami', 'Persian', 'Romanian', 'Slovenian', 'Thai', 'XCname', ...
+ 'en_family', 'nl_family', 'family_id', 'BreedingRange', 'BreedingSubRange', 'NonbreedingRange'};
if isempty(from_language)
%auto detect
- ndx=ismember(supportedlang,{'species_id','Order','Family','XCname',...
- 'en_family','family_id','BreedingRange','BreedingSubRange','NonbreedingRange'});
- supportedlang1=supportedlang(~ndx);
- species_id=[];
- for i=1:numel(supportedlang1)
- id=name2id(birdnames,supportedlang1{i});
- if numel(id)==numel(birdnames)
- from_language=supportedlang1{i};
- species_id=id;
- end
- end
- return;
+ ndx = ismember(supportedlang, {'species_id', 'Order', 'Family', 'XCname', ...
+ 'en_family', 'family_id', 'BreedingRange', 'BreedingSubRange', 'NonbreedingRange'});
+ supportedlang1 = supportedlang(~ndx);
+ species_id = [];
+ for i = 1:numel(supportedlang1)
+ id = name2id(birdnames, supportedlang1{i});
+ if numel(id) == numel(birdnames)
+ from_language = supportedlang1{i};
+ species_id = id;
+ end
+ end
+ return;
end
- from_language1=regexprep(from_language,'[\(\)]','_');
+ from_language1 = regexprep(from_language, '[\(\)]', '_');
%supportedlang = allbird_names.Properties.VariableNames;
ndx = strcmpi(from_language1, supportedlang);
if ~any(ndx)
supportedlang_user = supportedlang(~ismember(supportedlang, {'species_id', 'Order', 'XCname', 'Family'}));
- supportedlang_user=regexprep(supportedlang_user,'(.*)_(.*)_','$1($2)');
+ supportedlang_user = regexprep(supportedlang_user, '(.*)_(.*)_', '$1($2)');
s = sprintf('''%s'', ', supportedlang_user{:});
error('Language ''%s'' is not supported. supported languages are:\n%s\n', from_language, s);
else
from_language1 = supportedlang{ndx};
end
if isempty(birdnames)
- species_id=[];
+ species_id = [];
elseif exactfit
- if numel(birdnames)==1
- ndx=strcmpi(birdnames{1},allbird_names.(from_language1));
- species_id=allbird_names.species_id(ndx);
- else
- ndx2 = ismember(lower(allbird_names.(from_language1)),lower(birdnames));
- species_id = allbird_names.species_id(ndx2);
- end
+ if numel(birdnames)==1&&any(birdnames{1}==',')
+ birdnames=regexp(birdnames{1},'[ ]*,[ ]*','split');
+ end
+ ndx2 = matches(allbird_names.(from_language1), birdnames, 'ignorecase', true);
+ species_id = allbird_names.species_id(ndx2);
else
- ndx = contains(allbird_names.(from_language1),birdnames,'ignorecase',true);
- species_id = allbird_names.species_id(ndx);
+ %use wildcards like '*mees,koo?mees'
+ %wildcard symbols: * -any string
+ % ? -any character
+ % , -look for different patterns/species
+ pat = regexpPattern(regexprep(birdnames, {'[ ]*,[ ]*', '*', '?'}, {'|', '.*', '.'}), 'ignorecase', true);
+ ndx = matches(allbird_names.(from_language1), pat);
+ species_id = allbird_names.species_id(ndx);
end
-end
\ No newline at end of file
+end
diff --git a/bin/restore_database.m b/bin/restore_database.m
index 20acd5944416196754581876613a90026255e2cd..cd1db6672d8fe3ce7aa2df84db5894e9573a8a74 100644
--- a/bin/restore_database.m
+++ b/bin/restore_database.m
@@ -12,7 +12,7 @@ function [changedsettings] = restore_database(currfolder)
if nargin == 0
currfolder = 'curr';
end
- bird_settings = struct('filerec', [], 'selection', [], 'recs', [], 'deletedrecs', [], 'language', 'Dutch', 'currfolder', currfolder);
+ bird_settings = struct('filerec', [], 'recs', [], 'deletedrecs', [], 'language', 'Dutch', 'currfolder', currfolder);
changedsettings = true;
end
diff --git a/bin/selectrecords.m b/bin/selectrecords.m
index 65ea64f6643f46f8e1fe4ef8956281e0f2b4e93c..fdf0e585dbee87fb11c2c0e1e1cb063ced4fc9c4 100644
--- a/bin/selectrecords.m
+++ b/bin/selectrecords.m
@@ -1,4 +1,4 @@
-function [ndx, recs] = selectrecords(varargin)
+function [ndx, recs, opts] = selectrecords(varargin)
%first argument can be a struct/table (for instance bird_records)
%by default the records of bird_settings are selected.
% maxsamp - max sample size of the species in each group;
@@ -53,6 +53,10 @@ function [ndx, recs] = selectrecords(varargin)
% dvc - device
% mic - microphone type
% smp - sample rate
+ %
+ % ~ before the name is "not", for instance:
+ % ~id - exclude record ids
+
%load bird_settings bird_settings;
@@ -82,7 +86,13 @@ function [ndx, recs] = selectrecords(varargin)
if numel(varargin) > 0 && (rem(numel(varargin), 2) == 1)
varargin = ['autodetect', varargin];
end
-
+
+
+
+ if nargin == 0
+ ndx = true(size(recs, 1), 1);
+ return;
+ end
for i = 1:numel(varargin)
if isstring(varargin{i})
varargin{i} = cellstr(varargin{i});
@@ -99,26 +109,26 @@ function [ndx, recs] = selectrecords(varargin)
end
end
end
-
- if nargin == 0
- ndx = true(size(recs, 1), 1);
- return;
- end
-
-
+
allbird_names = evalin('base', 'allbird_names');
-
+
allbird_names_fields = fieldnames(allbird_names);
if ~isstruct(recs) && ~istable(recs)
recs_fields = {};
else
recs_fields = fieldnames(recs);
end
-
+
load localbirds localbirds
localbirds_fields = localbirds.Properties.VariableNames.';
opts = reshape(varargin, 2, numel(varargin) / 2);
+ notincluding = contains(opts(1, :), '~');
+ if any(notincluding)
+ opts(1, :) = regexprep(opts(1, :), '~', '');
+ end
+ opts(3, :) = num2cell(notincluding);
validoptions = [{'combine'; 'maxsamp'; 'year'; 'month'; 'hour'; 'language'; 'autodetect'}; recs_fields; allbird_names_fields; localbirds_fields];
+
ndx = ~ismember(lower(opts(1, :)), lower(validoptions));
if any(ndx)
s = sprintf('%s, ', validoptions{:});
@@ -133,6 +143,7 @@ function [ndx, recs] = selectrecords(varargin)
else
combfun = @(x)all(x,2); %and
end
+
ndx1 = strcmpi(opts(1, :), 'language');
if any(ndx1)
language = opts{2, ndx1};
@@ -186,7 +197,7 @@ function [ndx, recs] = selectrecords(varargin)
val1 = {val1};
end
switch field1
- case {'id', 'lat', 'lng', 'alt'}
+ case {'id', 'lat', 'lng', 'alt', 'length', 'bird_seen', 'playback_used', 'auto', 'smp', 'species_id'}
ndx(:, i) = numerical_value(val1, recs.(field1));
case {'type', 'sex', 'stage'}
ndx(:, i) = ismember_withcomma(val1, recs.(field1), field1);
@@ -210,7 +221,7 @@ function [ndx, recs] = selectrecords(varargin)
s = id2name(allbird_names.species_id(s), field1);
s = unique(s);
s = sprintf('''%s'', ', s{:});
- error('birdquiz:selectrecords:notfound', '%s=''%s'' is currently not in the database, valid options are:\n %s', field1, val1{:}, s);
+ error('birdquiz:selectrecords:notfound', '%s=''%s'' is currently not in the database, valid options are:\n %s\you can also use wildcards *?,\n', field1, val1{:}, s);
end
%ss = ismember(valids, [recs.species_id]);
%valids=valids(ss);
@@ -292,6 +303,10 @@ function [ndx, recs] = selectrecords(varargin)
ndx(:, i) = ismember(lower(recs.(field1)), lower(val1))';
end
end
+ notincluding = [opts{3, :}];
+ if any(notincluding)
+ ndx(:, notincluding) = ~ndx(:, notincluding);
+ end
ndx = combfun(ndx);
if ~isempty(maxsamp) && ~isinf(maxsamp)
%maxsamp random samples (if there are enough records
@@ -306,10 +321,13 @@ function [ndx, recs] = selectrecords(varargin)
ndx(fndx(fndx1)) = false;
end
end
-
+
end
function ndx = ismember_withcomma(val1, crecs, field1)
+ if iscell(val1) && numel(val1) == 1 && iscell(val1{1})
+ val1 = val1{1};
+ end
ndx = false(size(crecs));
if ~isempty(crecs)
for j = 1:numel(val1)
diff --git a/bin/selectspecies.m b/bin/selectspecies.m
index 432408036eb2499ba68eea8adca83a48a8279e9f..24eaaadef642a4565aaa2a20fdf05aab5583c23a 100644
--- a/bin/selectspecies.m
+++ b/bin/selectspecies.m
@@ -6,27 +6,20 @@ function selectspecies(varargin)
end
if isempty(bird_settings) && exist('bird_settings.mat', 'file')
load bird_settings bird_settings
- % bird_settings.selection=[];
- newselect = struct(varargin{:});
- % if isfield(bird_settings,'selection')&&~isempty(bird_settings.selection)&&isequal(newselect,bird_settings.selection)
- % disp('selection not changed');
- % return;
- % end
- bird_settings.selection = newselect;
else
- bird_settings = struct('selection', [], 'language', 'Dutch', 'currfolder', 'curr', ...
+ bird_settings = struct('language', 'Dutch', 'currfolder', 'curr', ...
'filerec', []);
end
% [bird_settings, deletedids, rec] = updatealldata(bird_settings);
restore_database;
rec = bird_settings.recs;
- bird_settings.selection = struct(varargin{:});
- save bird_settings bird_settings
-
+ %
+ opts=[];
if nargin > 0
try
- ndx = selectrecords(rec, varargin{:});
+ [ndx,~,opts] = selectrecords(rec, varargin{:});
+
% load bird_settings bird_settings
catch err
if strcmp(err.identifier, 'birdquiz:selectrecords:notfound')
@@ -45,7 +38,7 @@ function selectspecies(varargin)
restore_database;
rec = bird_settings.recs;
- ndx = selectrecords(varargin{:});
+ [ndx,~,opts] = selectrecords(varargin{:});
% load bird_settings bird_settings
else
rethrow(err);
@@ -55,6 +48,8 @@ function selectspecies(varargin)
else
selected = ~ismember([rec.id], bird_settings.deletedrecs);
end
+
+ % save bird_settings bird_settings
%load bird_settings bird_settings
bird_settings.filerec.selected=selected;
% c = num2cell(selected);
diff --git a/bin/sonogram.m b/bin/sonogram.m
index 81005983fc37dfc1228e84af3e3d2de0444dc971..fb27311e6a0e08f2a83ee4e0bded6e7de81ec682 100644
--- a/bin/sonogram.m
+++ b/bin/sonogram.m
@@ -1,5 +1,5 @@
function res = sonogram(filename, currtime)
-global bird_settings
+ global bird_settings
maxtime = 6;
if nargin == 1 && isnumeric(filename)
currtime = filename;
@@ -11,9 +11,9 @@ global bird_settings
%if isempty(get(hfig, 'KeyPressFcn'))
% set(hfig, 'KeyPressFcn', @keyPress)
%end
- warning('off','sonogram:toolboxmissing');
+ warning('off', 'sonogram:toolboxmissing');
sonogram(res, currtime);
- warning('on','sonogram:toolboxmissing');
+ warning('on', 'sonogram:toolboxmissing');
else
set(findobj(hfig, 'tag', 'timeline'), 'value', currtime);
drawnow;
@@ -61,17 +61,17 @@ global bird_settings
hfig = figwofocus(333);
set(hfig, 'userdata', res); %, 'visible', 'off');
-
+
if ~exist('spectrogram', 'file')
- warning('sonogram:toolboxmissing','The Signal Processing Toolbox is needed for creating a spectrogram, now plotting only the power plot ');
+ warning('sonogram:toolboxmissing', 'The Signal Processing Toolbox is needed for creating a spectrogram, now plotting only the power plot ');
ts = res.starttime + [0:numel(y) - 1]' ./ fs;
- S=[];
- hax=gca;
+ S = [];
+ hax = gca;
else
[ ~, f, t, S] = ...
spectrogram(y, 1000, 400, [], fs, 'yaxis');
S = 10 * log10(abs(S) + eps); %dB
-
+
try
hax = findobj(hfig, 'tag', 'subplot(1,1)');
catch
@@ -81,11 +81,11 @@ global bird_settings
hax = subplot(2, 1, 1);
end
%hax = subplot(2, 1, 1);
-
+
h = surf(hax, t + res.starttime, f / 1000, S);
set(h, 'tag', 'spectrogram');
set(hax, 'view', [0 90])
-
+
shading(hax, 'flat');
xlim(hax, [min(t + res.starttime) max(t + res.starttime)])
ylabel(hax, 'kHz')
@@ -105,7 +105,7 @@ global bird_settings
if isempty(hax)
hax = subplot(2, 1, 2);
end
-
+
end
h = plot(hax, ts, y);
set(h, 'tag', 'powerplot')
@@ -117,10 +117,10 @@ global bird_settings
xlim(hax, [min(ts) max(ts)])
% hfig = figwofocus(333);
if ~isempty(S)
- adjustplot(hfig, '-r')
- adjustplot(hfig, '-p', 0.02);
-
- set(hfig, 'position', [ 0.0219 0.2250 0.4367 0.6150])
+ adjustplot(hfig, '-r')
+ adjustplot(hfig, '-p', 0.02);
+
+ set(hfig, 'position', [ 0.0219 0.2250 0.4367 0.6150])
end
% set(hfig, 'visible', 'on');
end
@@ -147,12 +147,12 @@ end
% stopsound(4);
% end
% end
-
-function repeatsound(~, ~)
- global quest
- set(findobj(quest.h, 'tag', 'repeat'), 'visible', 'off')
- play(quest.player);
-end
+%
+% function repeatsound(~, ~)
+% global quest
+% set(findobj(quest.h, 'tag', 'repeat'), 'visible', 'off')
+% play(quest.player);
+% end
function hfig = figwofocus(nr)
try
hfig = findobj(groot, 'Number', nr);
diff --git a/bin/stopsound.m b/bin/stopsound.m
index bc1ab59c8f90404bf01c870da037017cceb8e29e..465daa0d1590d9430b4f7de416b43f2c76d25081 100644
--- a/bin/stopsound.m
+++ b/bin/stopsound.m
@@ -23,11 +23,13 @@ function stopsound(keuze)
if quest.current == keuze
quest.ncorrect = quest.ncorrect + 1;
h = msgbox(sprintf('Well done! It was indeed %s - %s (score=%d%%)', quest.common_name, quest.rec.type{1}, round(quest.ncorrect / quest.n * 100)), 'Succes');
+ drawnow
tic;
birdquiz('-getnext')
pause(2-toc);
else
h = msgbox(sprintf('Sorry that is not correct! It was %s (score=%d%%)', quest.common_name, round(quest.ncorrect / quest.n * 100)), 'Error', 'error');
+ drawnow
tic;
birdquiz('-getnext');
pause(3-toc);
diff --git a/birdquiz.m b/birdquiz.m
index 400caef5fa2dd223f73706b550ed193f41a9fdc8..e28875ef1f1543d2348fdf9bddfbf0c2555369e7 100644
--- a/birdquiz.m
+++ b/birdquiz.m
@@ -45,9 +45,7 @@ function birdquiz(varargin)
if restore_database
quest = [];
- end
-
-
+ end
if nargin > 0
if nargin == 2 && strcmpi(varargin{1}, 'language')
@@ -58,10 +56,7 @@ function birdquiz(varargin)
save bird_settings bird_settings
else
selectspecies(varargin{:});
- % load('bird_settings', 'bird_settings');
end
- else
- %load('bird_settings', 'bird_settings')
end
if isempty(quest)
diff --git a/makedatabase.m b/makedatabase.m
index df29bfd89acb4be61c0be041d2796d4fb7d2cb51..8d19658983d85b124d6a95c990007a77c17a79c9 100644
--- a/makedatabase.m
+++ b/makedatabase.m
@@ -4,7 +4,7 @@ function makedatabase(varargin)
%extra option:
%addmode - kind of add mode:
% 'reset' (default), removes all existing bird_records (after succesful download)
- % 'add' all the bird_records to the existing database
+ % 'add' add the bird_records to the existing database
% 'replace' replace selected species in the database
% 'tmp' keep it in a temporary folder, it will be deleted the next time
% you run makedatabase
@@ -28,7 +28,7 @@ function makedatabase(varargin)
if exist('bird_settings.mat', 'file')
load bird_settings bird_settings
else
- bird_settings = struct('selection', [], 'deletedrecs', [], 'language', 'Dutch', 'currfolder', 'curr', ...
+ bird_settings = struct( 'deletedrecs', [], 'language', 'Dutch', 'currfolder', 'curr', ...
'filerec', []);
save bird_settings bird_settings
end
diff --git a/runbatch.m b/runbatch.m
index 19cc1d631499bb1cbdb18b2b9e9a1c693eda3fa7..aab2361e413924a19677c515e4621a4105b1975e 100644
--- a/runbatch.m
+++ b/runbatch.m
@@ -9,9 +9,7 @@ if true
habitatgroups = cell(10, 1);
habitats = cell(10, 1);
j = 1;
-
-
-
+
habitats{j} = 'berg';
habitatgroups{j} = {'Slechtvalk', 'Boomleeuwerik', 'Appelvink', 'Fluiter', ...
'Middelste bonte specht', 'Vuurgoudhaan', 'Grauwe klauwier', ...
@@ -22,7 +20,7 @@ if true
habitats{j} = 'rivier';
habitatgroups{j} = {'Grote zilverreiger','Bergeend', 'Wilde Eend','Kleine zilverreiger', 'Ooievaar', ...
'Blauwe reiger', 'Grauwe gans', 'Brandgans', 'Kolgans','Oeverzwaluw', 'Koperwiek', ...
- 'Grote zaagbek', 'Smient', 'IJsvogel', 'Oeverloper','Nijlgans','Knobbelzwaan','Grote Canadese Gans'};
+ 'Grote zaagbek','Putter', 'Smient', 'IJsvogel', 'Oeverloper','Nijlgans','Knobbelzwaan','Grote Canadese Gans'};
j = j + 1;
habitats{j} = 'stad';
habitatgroups{j} = {'Huismus', 'Kauw', 'Ekster', 'Spreeuw', 'Zwarte kraai', ...