Fix misspelled code in documentation

Motion_Correction/other codes/MR_Log_demon_MC_batch.m

@@ -66,16 +66,3 @@
 
 
 
-opt{1,1}  = struct('niter',100, 'sigma_fluid',1,...
-    'sigma_diffusion',5, 'sigma_i',1,...
-    'sigma_x',1, 'do_display',plotme, 'do_plotenergy',plotme);
-opt{2,1} = struct('niter',100, 'sigma_fluid',1,...
-    'sigma_diffusion',5, 'sigma_i',1,...
-    'sigma_x',1, 'do_display',plotme, 'do_plotenergy',plotme);
-opt{3,1} = struct('niter',20, 'sigma_fluid',3,...
-    'sigma_diffusion',3, 'sigma_i',1,...
-    'sigma_x',1, 'do_display',plotme, 'do_plotenergy',plotme);
-opt{4,1} = struct('niter',20, 'sigma_fluid',3,...
-    'sigma_diffusion',3, 'sigma_i',1,...
-    'sigma_x',2, 'do_display',plotme, 'do_plotenergy',plotme);
-

Motion_Correction/other codes/frame_reg_PV.m

@@ -2,101 +2,101 @@
 % register movies with the hierarchical movement correction
 %   Jinghao Lu, 09/01/2017
 
-    hreg = tic;
-    %% initialization %%
-    %%% initialize parameters %%%
-    [pixh, pixw, nf] = size(m);
-
-    %%% prepare parallel computing %%%
-    if isempty(gcp('nocreate'))
-        parpool(feature('numCores'));
-    end
-    
-    %%% select gpu %%%
-    select_gpu;
-        
-    %%% preprocess Y first %%%
-    dthres = 0.1;
-    mskpre = uint8(dominant_patch(imaxn, dthres));
-    knl = fspecial('gaussian', [pixh, pixw], min(pixh, pixw) / 4);
-    maxallc = normalize(single(imaxn) .* knl);
-    maskc = uint8(normalize(imgaussfilt(feature2_comp(maxallc, 0, 100, 5), ...
-        100 * size(maxallc) / max(size(maxallc)))) > 0.4);
-    ttype = class(m(1, 1, 1));
-    stype = parse_type(ttype);
+hreg = tic;
+%% initialization %%
+%%% initialize parameters %%%
+[pixh, pixw, nf] = size(m);
+
+%%% prepare parallel computing %%%
+if isempty(gcp('nocreate'))
+    parpool(feature('numCores'));
+end
+
+%%% select gpu %%%
+select_gpu;
+
+%%% preprocess Y first %%%
+dthres = 0.1;
+mskpre = uint8(dominant_patch(imaxn, dthres));
+knl = fspecial('gaussian', [pixh, pixw], min(pixh, pixw) / 4);
+maxallc = normalize(single(imaxn) .* knl);
+maskc = uint8(normalize(imgaussfilt(feature2_comp(maxallc, 0, 100, 5), ...
+    100 * size(maxallc) / max(size(maxallc)))) > 0.4);
+ttype = class(m(1, 1, 1));
+stype = parse_type(ttype);
 %     nsize = pixh * pixw * nf * stype; %%% size of single %%%
 %     nbatch = batch_compute(nsize);
 %     ebatch = ceil(nf / nbatch);
 %     idbatch = [1: ebatch: nf, nf + 1];
 %     nbatch = length(idbatch) - 1;
-     m = m.*mskpre;
+m = m.*mskpre;
 
-    %%% get translation score %%%
-    fprintf('Begin initial computation of translation score \n')
-    nsize = pixh * pixw * nf * stype * 2; %%% size of single in parallel %%%
-    mq = 0.01;
+%%% get translation score %%%
+fprintf('Begin initial computation of translation score \n')
+nsize = pixh * pixw * nf * stype * 2; %%% size of single in parallel %%%
+mq = 0.01;
 
 
-   acorr= get_trans_score(m, [], 1, 1, mq, maskc);
+acorr= get_trans_score(m, [], 1, 1, mq, maskc);
 %         acorr(max(1, idbatch(i) - 1): idbatch(i + 1) - 2) = get_trans_score(tmp, [], 1, 1, mq);
-    end
+end
+
+%%% cluster movie into hierarchical stable-nonstable sections %%%
+[stt, stp, flag, scl, mc_flag] = hier_clust_PV(acorr, Fs, pixs, scl, stype, m); %%% flag: real or fake clusters %%%
+time = toc(hreg);
+fprintf(['Done initialization, ', num2str(time), ' seconds \n'])
 
-    %%% cluster movie into hierarchical stable-nonstable sections %%%
-    [stt, stp, flag, scl, mc_flag] = hier_clust_PV(acorr, Fs, pixs, scl, stype, m); %%% flag: real or fake clusters %%%
+if mc_flag
+    %% intra-section registration %%
+    fprintf('Begin intra-section \n')
+    m = intra_section_PV(m, stt, stp, pixs, scl, sigma_x, sigma_f, sigma_d, flag, maskc);
     time = toc(hreg);
-    fprintf(['Done initialization, ', num2str(time), ' seconds \n'])
-
-    if mc_flag
-        %% intra-section registration %%
-        fprintf('Begin intra-section \n')
-        m = intra_section_PV(m, stt, stp, pixs, scl, sigma_x, sigma_f, sigma_d, flag, maskc);
-        time = toc(hreg);
-        fprintf(['Done intra-section, ', num2str(time), ' seconds \n'])
-
-        %% update stable section %%
-        [sttn, stpn] = section_update(stt, stp, nf);
-
-        %% nonstable-section registration %%
-        fprintf('Begin nonstable-section \n')
-        m = nonstable_section(m, sttn, stpn, se, pixs, scl, sigma_x, sigma_f, sigma_d, maskc);
-        time = toc(hreg);
-        fprintf(['Done nonstable-section, ', num2str(time), ' seconds \n'])
-
-        %% inter-section registration %%
-        fprintf('Begin inter-section ... ')
-        m = inter_section(m, sttn, se, pixs, scl, sigma_x, sigma_f, sigma_d, maskc);
-        time = toc(hreg);
-        fprintf(['Done inter-section, ', num2str(time), ' seconds \n'])
-    end
-
-    %% spatiotemporal stabilization %%
-    m = frame_stab(m);
-
-    %% final preparation for output %%
-    %%% final score %%%
-    fprintf('Begin final computation of translation score \n')
-    nsize = pixh * pixw * nf * stype * 2; %%% size of single in parallel %%%
-    nbatch = batch_compute(nsize);
-    ebatch = ceil(nf / nbatch);
-    idbatch = [1: ebatch: nf, nf + 1];
-    nbatch = length(idbatch) - 1;
-    acorrf = zeros(1, nf - 1);
-    imax = zeros(pixh, pixw);
-    mx = 0;
-    mn = 0;
-    for i = 1: nbatch
-        tmp = m.reg(1: pixh, 1: pixw, max(1, idbatch(i) - 1): idbatch(i + 1) - 1);
-        acorrf(max(1, idbatch(i) - 1): idbatch(i + 1) - 2) = get_trans_score(tmp, [], 1, 1, [], maskc);
-        mx = max(mx, max(max(max(tmp, [], 1), [], 2), [], 3));
-        mn = min(mx, min(max(min(tmp, [], 1), [], 2), [], 3));
-        imax = max(imax, max(tmp, [], 3));
-    end
-    imax = imax - mn;
-    imax = imax / (mx - mn);
-
-    %%% normalize %%%
-    m = normalize_batch(m.Properties.Source, 'reg', mx, mn, idbatch);
+    fprintf(['Done intra-section, ', num2str(time), ' seconds \n'])
+
+    %% update stable section %%
+    [sttn, stpn] = section_update(stt, stp, nf);
+
+    %% nonstable-section registration %%
+    fprintf('Begin nonstable-section \n')
+    m = nonstable_section(m, sttn, stpn, se, pixs, scl, sigma_x, sigma_f, sigma_d, maskc);
     time = toc(hreg);
-    fprintf(['Done frame reg, total time: ', num2str(time), ' seconds \n'])
+    fprintf(['Done nonstable-section, ', num2str(time), ' seconds \n'])
+
+    %% inter-section registration %%
+    fprintf('Begin inter-section ... ')
+    m = inter_section(m, sttn, se, pixs, scl, sigma_x, sigma_f, sigma_d, maskc);
+    time = toc(hreg);
+    fprintf(['Done inter-section, ', num2str(time), ' seconds \n'])
+end
+
+%% spatiotemporal stabilization %%
+m = frame_stab(m);
+
+%% final preparation for output %%
+%%% final score %%%
+fprintf('Begin final computation of translation score \n')
+nsize = pixh * pixw * nf * stype * 2; %%% size of single in parallel %%%
+nbatch = batch_compute(nsize);
+ebatch = ceil(nf / nbatch);
+idbatch = [1: ebatch: nf, nf + 1];
+nbatch = length(idbatch) - 1;
+acorrf = zeros(1, nf - 1);
+imax = zeros(pixh, pixw);
+mx = 0;
+mn = 0;
+for i = 1: nbatch
+    tmp = m.reg(1: pixh, 1: pixw, max(1, idbatch(i) - 1): idbatch(i + 1) - 1);
+    acorrf(max(1, idbatch(i) - 1): idbatch(i + 1) - 2) = get_trans_score(tmp, [], 1, 1, [], maskc);
+    mx = max(mx, max(max(max(tmp, [], 1), [], 2), [], 3));
+    mn = min(mx, min(max(min(tmp, [], 1), [], 2), [], 3));
+    imax = max(imax, max(tmp, [], 3));
+end
+imax = imax - mn;
+imax = imax / (mx - mn);
+
+%%% normalize %%%
+m = normalize_batch(m.Properties.Source, 'reg', mx, mn, idbatch);
+time = toc(hreg);
+fprintf(['Done frame reg, total time: ', num2str(time), ' seconds \n'])
 end
 

docs/Prep.md

@@ -27,7 +27,7 @@ The function used to downsample video sessions would depende on the format of th
 
 === ".isdx (Inscopix)"
 	``` matlab
-	Downsample_inscopix(ds_f, outpath, theFiles)
+	Downsample_Inscopix(ds_f, outpath, theFiles)
 	```
 	This function reads Inscopix video files, downsamples them, and saves the resulting frames as an HDF5 (.h5) file.
 

docs/TLDR.md

@@ -20,7 +20,7 @@ Run the following functions:
 	```	
 === ".isdx (Inscopix)"
 	``` matlab
-	Downsample_inscopix(4)
+	Downsample_Inscopix(4)
 	```
 
 ### 2) Motion Correction: