auto spatialr and se detect function

JinghaoLu · Mar 25, 2022 · ce0e1f1 · ce0e1f1
1 parent e210363
commit ce0e1f1
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Showing 4 changed files with 52 additions and 13 deletions.
diff --git a/min1pipe.m b/min1pipe.m
@@ -10,23 +10,20 @@
     min1pipe_init;
 
     %% initialize parameters %%
+    defpar = default_parameters;
     if nargin < 1 || isempty(Fsi)
-        defpar = default_parameters;
         Fsi = defpar.Fsi;
     end
 
     if nargin < 2 || isempty(Fsi_new)
-        defpar = default_parameters;
         Fsi_new = defpar.Fsi_new;
     end
 
     if nargin < 3 || isempty(spatialr)
-        defpar = default_parameters;
         spatialr = defpar.spatialr;
     end
 
     if nargin < 4 || isempty(se)
-        defpar = default_parameters;
         se = defpar.neuron_size;
     end
 
@@ -69,7 +66,12 @@
 
     hpipe = tic;
     for i = 1: length(file_base)
-
+        %%% auto-detect/adjust parameters %%%
+        fname = [path_name, file_base{i}, '.', file_fmt{i}];
+        [se, spatialr] = frame_sample(fname);
+        Params.neuron_size = se;
+        Params.spatialr = spatialr;
+
         %%% judge whether do the processing %%%
         filecur = [path_name, file_base{i}, '_data_processed.mat'];
         msg = 'Redo the analysis? (y/n)';

diff --git a/min1pipe_HPC.m b/min1pipe_HPC.m
@@ -10,23 +10,20 @@
     min1pipe_init;
 
     %% initialize parameters %%
+    defpar = default_parameters;
     if nargin < 1 || isempty(Fsi)
-        defpar = default_parameters;
         Fsi = defpar.Fsi;
     end
 
     if nargin < 2 || isempty(Fsi_new)
-        defpar = default_parameters;
         Fsi_new = defpar.Fsi_new;
     end
 
     if nargin < 3 || isempty(spatialr)
-        defpar = default_parameters;
         spatialr = defpar.spatialr;
     end
 
     if nargin < 4 || isempty(se)
-        defpar = default_parameters;
         se = defpar.neuron_size;
     end
 
@@ -38,10 +35,6 @@
         flag = 1;
     end
 
-    if nargin < 7 || isempty(flag)
-        [file_name, path_name] = uigetfile('*', 'Select coordinates file', 'MultiSelect', 'on');
-    end
-
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     %%%%%%%%%%%%%%%%%%%%%%%%%% parameters %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     %%% user defined parameters %%%                                     %%%
@@ -73,6 +66,11 @@
 
     hpipe = tic;
     for i = 1: length(file_base)
+        %%% auto-detect/adjust parameters %%%
+        fname = [path_name, file_base{i}, '.', file_fmt{i}];
+        [se, spatialr] = frame_sample(fname);
+        Params.neuron_size = se;
+        Params.spatialr = spatialr;
 
         %%% judge whether do the processing %%%
         filecur = [path_name, file_base{i}, '_data_processed.mat'];

diff --git a/utilities/elements/auto_detect_params.m b/utilities/elements/auto_detect_params.m
@@ -0,0 +1,18 @@
+function s = auto_detect_params(a)
+    aa = a - imgaussfilt(a, min(size(a)) / 5);
+    aa = max(mean(aa(:)), aa);
+    aaa = imgaussfilt(aa,2);
+    scl = 5;
+    b = sort(aaa(:))';
+    bb = b - scl * linspace(min(aaa(:)), max(aaa(:)), numel(aaa));
+    [~, id] = min(bb);
+    thres = b(id);
+    bbb = imopen(aaa > thres, strel('disk', 2));
+    [l, n] = bwlabeln(bbb);
+    s = zeros(1, n);
+    for i = 1: n
+        tmp = l == i;
+        st = sum(tmp(:));
+        s(i) = sqrt(st / pi);
+    end
+end
diff --git a/utilities/elements/frame_sample.m b/utilities/elements/frame_sample.m
@@ -0,0 +1,21 @@
+function [se, spatialr] = frame_sample(m)
+    f = imfinfo(m);
+    n = length(f);
+    nu = min(100, n);
+    s = cell(1, nu);
+    id = randsample(n, nu);
+    for i = 1: nu
+        tmp = double(imread(m, id(i)));
+        st = auto_detect_params(tmp);
+        s{i} = st;
+    end
+    s = cell2mat(s);
+    sf = floor(mean(s));
+    if sf > 6
+        spatialr = 3 / sf;
+        se = 5;
+    else
+        spatialr = 1;
+        se = sf;
+    end
+end