Fix some important bugs

CaliAli-PV · Sep 10, 2024 · a9c7c2b · a9c7c2b
1 parent f37e9ff
commit a9c7c2b
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Showing 5 changed files with 9 additions and 4 deletions.
diff --git a/Align_sessions/int_var.m b/Align_sessions/int_var.m
@@ -13,6 +13,7 @@
                                          %Size of blood vessels [min diameter max diameter] in pixels. 
 addParameter(inp,'FinalAlignmentWithNeuronShapes',0)    % Add an extra alignment iteration utilizing only neuron shapes after CaliAli
 addParameter(inp,'Force_BVz',0)          % Fore the use of BVz for alignment, even if BVz stability score is low.
+addParameter(inp,'batch_sz',0)           % Number of frames to use per batch. If batch_sz=0, then the number of frame per batch is equal to the number of frames per_session.
 %%                                         
 addParameter(inp,'dynamic_spatial',0)    % not currently in use                                   
 addParameter(inp,'datename',0)           % not currently in use

diff --git a/CNMF-e/CaliAli_modified_codes/scale_to_noise.m b/CNMF-e/CaliAli_modified_codes/scale_to_noise.m
@@ -1,8 +1,8 @@
 function scale_to_noise(neuron)
 %  We estimate the noise from the remnant between the raw and deconvolved calcium trace.
 % we use a moving window of size=num
-if size(neuron.options.F,2)>1
-    c=cumsum(neuron.options.F)';
+if size(get_batch_size(neuron,0),2)>1
+    c=cumsum(get_batch_size(neuron,0))';
     c=[[0;c(1:end-1)]+1,c];
 else
     c=[neuron.frame_range(1),neuron.frame_range(2)];

diff --git a/CNMF-e/CaliAli_modified_codes/update_residual_Cn_PNR_batch.m b/CNMF-e/CaliAli_modified_codes/update_residual_Cn_PNR_batch.m
@@ -12,7 +12,7 @@
 d2=neuron.options.d2;
 gSig=neuron.options.gSig;
 n_enhanced=neuron.n_enhanced;
-fn=[0,cumsum(neuron.options.F)];
+fn=[0,cumsum(get_batch_size(neuron,0))];
 for i=progress(1:size(fn,2)-1)
     Y = neuron.load_patch_data([],[fn(i)+1,fn(i+1)]);
     if ~ismatrix(Y); Y = reshape(Y, d1*d2, []); end % convert the 3D movie to a matrix

diff --git a/CNMF-e/runCNMFe.m b/CNMF-e/runCNMFe.m
@@ -188,7 +188,7 @@ function runCNMFe(in,PNR_th,Coor_th,gSig,sf)
 
 %% Optional post-process
 scale_to_noise(neuron);
-neuron.C_raw=detrend_Ca_traces(neuron.Fs*2,neuron.C_raw,neuron.CaliAli_opt.F);
+neuron.C_raw=detrend_Ca_traces(neuron.Fs*2,neuron.C_raw,get_batch_size(neuron));
 justdeconv(neuron,'thresholded','ar2',0);
 denoise_thresholded(neuron,5);
 

diff --git a/Other_codes/Experimental/get_batch_size.m b/Other_codes/Experimental/get_batch_size.m
@@ -5,6 +5,10 @@
 end
 F=neuron.CaliAli_opt.F;
 
+if neuron.CaliAli_opt.batch_sz>0
+    F=diff(round(linspace(1,sum(F),round(sum(F)/neuron.CaliAli_opt.batch_sz)+1)));
+end
+
 if neuron.CaliAli_opt.dynamic_spatial==1
     ses=20;
     if length(F)<ses