Merge pull request #220 from Julie-Fabre/bleeding_edge_matlab

update gui
Julie-Fabre · Nov 25, 2024 · 2999f1e · 2999f1e
2 parents 13dbac3 + e681a97
commit 2999f1e
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diff --git a/+bc/+qm/qualityParamValuesForUnitMatch.m b/+bc/+qm/qualityParamValuesForUnitMatch.m
@@ -68,8 +68,8 @@
 
 % refractory period parameters - change closer together
 paramBC.tauR_valuesMin = 2/1000; % refractory period time (s), usually 0.0020 change
-paramBC.tauR_valuesStep = 0.5./1000; % refractory period time (s), usually 0.0020
-paramBC.tauR_valuesMax = 2./1000; % refractory period time (s), usually 0.0020
+paramBC.tauR_valuesStep = 0.5/1000; % refractory period time (s), usually 0.0020
+paramBC.tauR_valuesMax = 2/1000; % refractory period time (s), usually 0.0020
 paramBC.tauC = 0.1/1000; % censored period time (s)
 paramBC.hillOrLlobetMethod = 1; % 1 to use Hill et al method; 0 to use Llobet et al method
 

diff --git a/+bc/+viz/unitQualityGUI_synced.m b/+bc/+viz/unitQualityGUI_synced.m
@@ -71,7 +71,6 @@ function KeyPressCb(~, evnt)
 
 
         elseif strcmpi(evnt.Key, 'g') %toggle to next single-unit
-            iCluster = iCluster + 1;
             iCluster = goodUnit_idx(find(goodUnit_idx > iCluster, 1, 'first')); 
             if ~isempty(iCluster)
                 updateUnit(unitQualityGuiHandle, memMapData, ephysData, rawWaveforms, iCluster, qMetric, forGUI, param, ...
@@ -80,7 +79,6 @@ function KeyPressCb(~, evnt)
                 disp('Done cycling through good units.')
             end
         elseif strcmpi(evnt.Key, 'm') %toggle to next multi-unit
-            iCluster = iCluster + 1;
             iCluster = multiUnit_idx(find(multiUnit_idx > iCluster, 1, 'first'));
             if ~isempty(iCluster)
             updateUnit(unitQualityGuiHandle, memMapData, ephysData, rawWaveforms, iCluster, qMetric, forGUI, param, ...
@@ -89,7 +87,6 @@ function KeyPressCb(~, evnt)
                 disp('Done cycling through MUA units.')
             end
         elseif strcmpi(evnt.Key, 'n') %toggle to next  noise unit
-            iCluster = iCluster + 1;
             iCluster = noiseUnit_idx(find(noiseUnit_idx > iCluster, 1, 'first'));
             if ~isempty(iCluster)
             updateUnit(unitQualityGuiHandle, memMapData, ephysData, rawWaveforms, iCluster, qMetric, forGUI, param, ...
@@ -98,7 +95,6 @@ function KeyPressCb(~, evnt)
                 disp('Done cycling through noise units.')
             end
        elseif strcmpi(evnt.Key, 'a') %toggle to next  non-somatic unit
-           iCluster = iCluster + 1;
             iCluster = nonSomaUnit_idx(find(nonSomaUnit_idx > iCluster, 1, 'first'));
             if ~isempty(iCluster)
             updateUnit(unitQualityGuiHandle, memMapData, ephysData, rawWaveforms, iCluster, qMetric, forGUI, param, ...
@@ -278,7 +274,7 @@ function initializePlot(unitQualityGuiHandle, ephysData, qMetric, unitType, uniq
     'filled', 'MarkerEdgeColor', [0, 0, 0], 'LineWidth', 4);
 xlim([-0.1, 1.1]);
 ylim([min(ephysData.channel_positions(:, 2)) - 50, max(ephysData.channel_positions(:, 2)) + 50]);
-ylabel('Depth (\mum)')
+ylabel('Depth from tip of probe (\mum)')
 xlabel('Norm. log rate')
 %title('Location on probe')
 

diff --git a/docs/images/bombcell_flowchart.svg b/docs/images/bombcell_flowchart.svg
diff --git a/gettingStarted.mlx b/gettingStarted.mlx
diff --git a/toy_data/cluster_bc_unitType.tsv b/toy_data/cluster_bc_unitType.tsv
@@ -9,7 +9,7 @@ cluster_id	bc_unitType
 7	MUA
 8	MUA
 9	MUA
-10	GOOD
+10	MUA
 11	NON-SOMA
 12	MUA
 13	GOOD

diff --git a/toy_data/cluster_frac_RPVs.tsv b/toy_data/cluster_frac_RPVs.tsv
@@ -4,13 +4,13 @@ cluster_id	frac_RPVs
 2	1
 3	1
 4	1
-5	0.982237865269706
-6	0.0329025217284871
+5	0.982543477548881
+6	0.0329225611958505
 7	1
-8	0.676498444053579
+8	0.683526999316473
 9	1
 10	0
 11	0
 12	1
 13	0
-14	0.408260607079116
+14	0.408965264898236
diff --git a/toy_data/cluster_percentage_spikes_missing.tsv b/toy_data/cluster_percentage_spikes_missing.tsv
@@ -1,16 +1,16 @@
 cluster_id	percentage_spikes_missing
-0	38.1967017426773
-1	42.8281872928592
+0	38.163390555602
+1	42.8402542605489
 2	50.0000000000004
-3	23.5647964841725
+3	23.5898660439423
 4	50.0000000000002
-5	5.10158447383244
-6	9.53487466759384e-07
+5	5.09288406956974
+6	9.5231732499812e-07
 7	50.0000000000001
-8	0.688108894496897
-9	50.0000000000002
-10	0.000408992541811593
-11	0.139116235780157
+8	0.610287410911903
+9	50.0000000000001
+10	0.000221642010145295
+11	0.120072043634112
 12	50
-13	12.7921675746407
-14	2.61164141506351
+13	12.9690219382565
+14	2.60336213594937
diff --git a/toy_data/cluster_presence_ratio.tsv b/toy_data/cluster_presence_ratio.tsv
@@ -8,8 +8,8 @@ cluster_id	presence_ratio
 6	0.824324324324324
 7	0.689189189189189
 8	0.864864864864865
-9	0.337837837837838
-10	0.716216216216216
+9	0.324324324324324
+10	0.689189189189189
 11	0.824324324324324
 12	1
 13	0.932432432432432

diff --git a/toy_data/qMetrics/_bc_parameters._bc_qMetrics.parquet b/toy_data/qMetrics/_bc_parameters._bc_qMetrics.parquet
diff --git a/toy_data/qMetrics/templates._bc_fractionRefractoryPeriodViolationsPerTauR.parquet b/toy_data/qMetrics/templates._bc_fractionRefractoryPeriodViolationsPerTauR.parquet
diff --git a/toy_data/qMetrics/templates._bc_qMetrics.parquet b/toy_data/qMetrics/templates._bc_qMetrics.parquet
diff --git a/toy_data/qMetrics/templates.qualityMetricDetailsforGUI.mat b/toy_data/qMetrics/templates.qualityMetricDetailsforGUI.mat
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,7 +9,7 @@ cluster_id bc_unitType @@
 	MUA
 	MUA
 	MUA
-	GOOD
+	MUA
 	NON-SOMA
 	MUA
 	GOOD
@@ Expand Down @@