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Adding CellBase-specific Preferences #8

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May 8, 2018
Merged

Adding CellBase-specific Preferences #8

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5657292
Cellbase-specific preferences are now saved in PREFERENCES variable i…
torbenott May 2, 2018
6f05f26
minor improvements.
torbenott May 2, 2018
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4 changes: 2 additions & 2 deletions CellBase_R2013a/AddOns/AnalysisFcn_AK_SPR/plotting/plot_mclust_projections.m
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Expand Up @@ -8,7 +8,7 @@ function plot_mclust_projections(cellid)
% Only the first light evoked spike is selected for plotting. To account
% for drift, only spikes during the stimulation protocol are selected for
% plotting.
% SPR 2011-12-28
% SPR 2011-12-28, TO 5/2018

if nargin < 1,
help plot_mclust_projections
Expand Down Expand Up @@ -47,7 +47,7 @@ function plot_mclust_projections(cellid)
prop = 'Energy.fd';
% prop = 'Peak.fd';

propfn = [getpref('cellbase','cell_pattern') num2str(t) '_' prop];
propfn = [getcbpref('Spikes_cell_pattern') num2str(t) '_' prop];
propfn_path = [cellid2fnames(cellid,'sess') filesep propfn];
wf_prop = load(propfn_path,'-mat');
wf_prop1 = wf_prop.FeatureData(:,1);
Expand Down
6 changes: 3 additions & 3 deletions CellBase_R2013a/Functions/analysis_functions/optical_tagging/lightcluster.m
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Expand Up @@ -21,7 +21,7 @@
% [email protected]
% 09-May-2012

% Edit log: BH 5/9/12, 6/20/12
% Edit log: BH 5/9/12, 6/20/12, TO 5/2018

% Input arguments
prs = inputParser;
Expand All @@ -40,7 +40,7 @@
% Load spikes from Ntt file.
Nttfn = cellid2fnames(cellid,'Ntt');
all_spikes = LoadTT_NeuralynxNT(Nttfn);
TIMEFACTOR = getpref('cellbase','timefactor'); % scaling factor to convert spike times into seconds
TIMEFACTOR = getcbpref('Spikes_timefactor'); % scaling factor to convert spike times into seconds
all_spikes = all_spikes * TIMEFACTOR;
spk = loadcb(cellid,'Spikes');

Expand Down Expand Up @@ -71,7 +71,7 @@
valid_channels = check_channel_validity(cellid); % valid channels
X = [];
for k = 1:length(g.feature_names)
basename = [getpref('cellbase','cell_pattern') num2str(t)];
basename = [getcbpref('Spikes_cell_pattern') num2str(t)];
propfn = [basename '_' g.feature_names{k}]; % name of feature file (e.g. TT1_Amplitude)
sessionpath = cellid2fnames(cellid,'sess');
propfn_path = [sessionpath filesep 'FD']; % where the feature file can be found
Expand Down
4 changes: 2 additions & 2 deletions CellBase_R2013a/Functions/analysis_functions/spike_clusters/LRatio.m
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Expand Up @@ -28,7 +28,7 @@
% Load Ntt file
Nttfn = cellid2fnames(cellid,'Ntt');
all_spikes = LoadTT_NeuralynxNT(Nttfn);
TIMEFACTOR = getpref('cellbase','timefactor'); % scaling factor to convert spike times into seconds
TIMEFACTOR = getcbpref('Spikes_timefactor'); % scaling factor to convert spike times into seconds
all_spikes = all_spikes * TIMEFACTOR;
spk = loadcb(cellid,'Spikes');
n = length(all_spikes); % avoid subsampling of spikes due to rounding errors
Expand All @@ -43,7 +43,7 @@
% Feature matrix
X = [];
for k = 1:length(feature_names)
basename = [getpref('cellbase','cell_pattern') num2str(t)];
basename = [getcbpref('Spikes_cell_pattern') num2str(t)];
propfn = [basename '_' feature_names{k}]; % name of feature file (e.g. TT1_Amplitude)
sessionpath = cellid2fnames(cellid,'sess');
propfn_path = [sessionpath filesep 'FD']; % where the feature file can be found
Expand Down
4 changes: 2 additions & 2 deletions CellBase_R2013a/Functions/analysis_functions/spike_clusters/LRatio2.m
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Expand Up @@ -36,7 +36,7 @@
% Load Ntt file
Nttfn = cellid2fnames(cellid,'Ntt');
all_spikes = LoadTT_NeuralynxNT(Nttfn);
TIMEFACTOR = getpref('cellbase','timefactor'); % scaling factor to convert spike times into seconds
TIMEFACTOR = getcbpref('Spikes_timefactor'); % scaling factor to convert spike times into seconds
all_spikes = all_spikes * TIMEFACTOR;
spk = loadcb(cellid,'Spikes');
n = length(all_spikes);
Expand All @@ -49,7 +49,7 @@
% Feature matrix
X = [];
for k = 1:length(g.feature_names)
basename = [getpref('cellbase','cell_pattern') num2str(t)];
basename = [getcbpref('Spikes_cell_pattern') num2str(t)];
propfn = [basename '_' g.feature_names{k}]; % name of feature file (e.g. TT1_Amplitude)
sessionpath = cellid2fnames(cellid,'sess');
propfn_path = [sessionpath filesep 'FD']; % where the feature file can be found
Expand Down
2 changes: 1 addition & 1 deletion CellBase_R2013a/Functions/analysis_functions/spike_clusters/check_channel_validity.m
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Expand Up @@ -13,7 +13,7 @@
[r,s,t,u] = cellid2tags(cellid);

% Load Energy
propfn = [getpref('cellbase','cell_pattern') num2str(t) '_Energy'];
propfn = [getcbpref('Spikes_cell_pattern') num2str(t) '_Energy'];
propfn_path = [cellid2fnames(cellid,'sess') filesep 'FD'];
if ~isdir(propfn_path)
propfn_path = cellid2fnames(cellid,'sess');
Expand Down
4 changes: 2 additions & 2 deletions CellBase_R2013a/Functions/analysis_functions/spike_clusters/plot_mclust_projections2.m
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Expand Up @@ -66,7 +66,7 @@
% Load spikes from Ntt file.
Nttfn = cellid2fnames(cellid,'Ntt');
all_spikes = LoadTT_NeuralynxNT(Nttfn);
TIMEFACTOR = getpref('cellbase','timefactor'); % scaling factor to convert spike times into seconds
TIMEFACTOR = getcbpref('Spikes_timefactor'); % scaling factor to convert spike times into seconds
all_spikes = all_spikes * TIMEFACTOR;
val_spk_i = [find(all_spikes >= pon(1),1,'first') ...
find(all_spikes <= pon(end),1,'last')]; % consider spikes only within the stimulation protocol to account for drift
Expand Down Expand Up @@ -101,7 +101,7 @@
[r,s,t] = cellid2tags(cellid);
for k = 1:length(g.feature_names)
prop = [g.feature_names{k} '.fd'];
propfn = [getpref('cellbase','cell_pattern') num2str(t) '_' prop];
propfn = [getcbpref('Spikes_cell_pattern') num2str(t) '_' prop];
sessionpath = cellid2fnames(cellid,'sess');
propfn_path = [sessionpath filesep 'FD']; % where the feature file can be found
if ~isdir(propfn_path)
Expand Down
2 changes: 1 addition & 1 deletion CellBase_R2013a/Functions/data_processing_functions/MakeTrialEvents2_gonogo.m
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Expand Up @@ -9,7 +9,7 @@ function MakeTrialEvents2_gonogo(sessionpath,varargin)
% file becomes the primary store of behavioral data for a particular
% session; it is retrieved by LOADCB via CELLID2FNAMES. This default
% file name is one of the preference settings of CellBase - type
% getpref('cellbase','session_filename');
% getcbpref('TrialEvents_filename');
%
% MAKETRIALEVENTS2_GONOGO(SESSIONPATH,'StimNttl',TTL) specifies the TTL
% channel which serves as the basis for synchronization.
Expand Down
2 changes: 1 addition & 1 deletion CellBase_R2013a/Functions/data_processing_functions/extractSpikeWaveforms.m
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Expand Up @@ -37,7 +37,7 @@

% Load waveform data (Ntt file)
Nttfile = cellid2fnames(cellid,'ntt');
TIMEFACTOR = getpref('cellbase','timefactor'); % scaling factor to convert spike times into seconds
TIMEFACTOR = getcbpref('Spikes_timefactor'); % scaling factor to convert spike times into seconds
[all_spikes all_waves] = LoadTT_NeuralynxNT(Nttfile);
[junk junk2 evoked_inx] = intersect(SpikeTimes,all_spikes*TIMEFACTOR);
if ~isequal(junk,SpikeTimes) % internal check for spike times
Expand Down
2 changes: 1 addition & 1 deletion CellBase_R2013a/Functions/database_functions/analyses/addanalysis.m
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Expand Up @@ -163,7 +163,7 @@ function addanalysis(funhandle,varargin)
copyfile(cb,backup_name) % make backup before overwriting

% SAVE CELLBASE
save(getpref('cellbase','fname'),'TheMatrix','ANALYSES','CELLIDLIST')
save(getpref('cellbase','fname'),'TheMatrix','ANALYSES','CELLIDLIST','PREFERENCES')

% -------------------------------------------------------------------------
function ts = timestamp
Expand Down
4 changes: 2 additions & 2 deletions CellBase_R2013a/Functions/database_functions/analyses/delanalysis.m
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Expand Up @@ -9,7 +9,7 @@ function delanalysis(funhandle)
%
% See also ADDANALYSIS and FINDANALYSIS.

% Edit log: BH 6/21/12
% Edit log: BH 6/21/12, TO 5/2018

% Load CellBase
load(getpref('cellbase','fname'));
Expand Down Expand Up @@ -73,4 +73,4 @@ function delanalysis(funhandle)
dsr = regexprep(dsr,':','_');
backup_name = fullfile(pth,[fnm '_' dsr ext]);
copyfile(cb,backup_name) % make backup before overwriting
save(getpref('cellbase','fname'),'TheMatrix','ANALYSES','CELLIDLIST')
save(getpref('cellbase','fname'),'TheMatrix','ANALYSES','CELLIDLIST','PREFERENCES')
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