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thresholded_8_CDH_2_original_stripes.m
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thresholded_8_CDH_2_original_stripes.m
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%R_border=470;
%R_bulk=3/4*R_border;
%R_core=R_border/4;
R_core=50;
R_bulk_1=200;
R_bulk_2=250;
R_border_1=420;
R_border_2=470;
num_prof_points=50;
dR=R_border_2/num_prof_points;
pivobj_CDH_2_mg_blured_stripes_thr8=cell(1,5);
fldr_CDH_2_mg_master_thrsh8_orig=...
'/Volumes/Seagate Expansion Drive/workspace/Circular_Cells/OriginalTIFF/CDH2_' ;
av_vel_profile_bluredCDH_2_stripes_thr8=cell(1,5);
av_curlz_profile_bluredCDH_2_stripes_thr8=cell(1,5);
av_div_profile_bluredCDH_2_stripes_thr8=cell(1,5);
vxs_core_all_t_CDH_2_mg_blured_stripes_thr8=cell(1,5);
vys_core_all_t_CDH_2_mg_blured_stripes_thr8=cell(1,5);
vxs_bulk_all_t_CDH_2_mg_blured_stripes_thr8=cell(1,5);
vys_bulk_all_t_CDH_2_mg_blured_stripes_thr8=cell(1,5);
vxs_border_all_t_CDH_2_mg_blured_stripes_thr8=cell(1,5);
vys_border_all_t_CDH_2_mg_blured_stripes_thr8=cell(1,5);
vort_core_CDH_2_mg_blured_stripes_thr8=cell(1,5);
vort_bulk_CDH_2_mg_blured_stripes_thr8=cell(1,5);
vort_border_CDH_2_mg_blured_stripes_thr8=cell(1,5);
for i=1:5
av_vel_profile_bluredCDH_2_stripes_thr8{i}=zeros(1,num_prof_points);
av_curlz_profile_bluredCDH_2_stripes_thr8{i}=zeros(1,num_prof_points);
av_div_profile_bluredCDH_2_stripes_thr8{i}=zeros(1,num_prof_points);
fldr_CDH_2_mg_h=[fldr_CDH_2_mg_master_thrsh8_orig num2str(i) '_from_tif/'];
fls_CDH_2mg_h=dir([fldr_CDH_2_mg_h 'blured*.txt']);
data_test=importdata(...
[fldr_CDH_2_mg_h fls_CDH_2mg_h(1).name]);
len = length(data_test.data);
pivobj_CDH_2_mg_blured_stripes_thr8{i}.xs=zeros(len, length(fls_CDH_2mg_h));
pivobj_CDH_2_mg_blured_stripes_thr8{i}.ys=zeros(len, length(fls_CDH_2mg_h));
pivobj_CDH_2_mg_blured_stripes_thr8{i}.vxs=zeros(len, length(fls_CDH_2mg_h));
pivobj_CDH_2_mg_blured_stripes_thr8{i}.vys=zeros(len, length(fls_CDH_2mg_h));
for t=1:length(fls_CDH_2mg_h)
data_test=importdata(...
[fldr_CDH_2_mg_h fls_CDH_2mg_h(t).name]);
pivobj_CDH_2_mg_blured_stripes_thr8{i}.xs(:,t) = data_test.data(:,1);
pivobj_CDH_2_mg_blured_stripes_thr8{i}.ys(:,t) = data_test.data(:,2);
pivobj_CDH_2_mg_blured_stripes_thr8{i}.vxs(:,t) = data_test.data(:,3);
pivobj_CDH_2_mg_blured_stripes_thr8{i}.vys(:,t) = data_test.data(:,4);
end
[pivX_CDH_2mg_blured_thr, pivY_CDH_2mg_blured_thr,...
pivVX_CDH_2mg_blured_thr, pivVY_CDH_2mg_blured_thr,...
pivDIV_CDH_2mg_blured_thr, pivDIVall_CDH_2mg_blured_thr,...
pivCURLz_CDH_2mg_blured_thr, pivCURLav_CDH_2mg_blured_thr,...
pivCURLz_all_CDH_2mg_blured_thr, pivCURLav_all_CDH_2mg_blured_thr] = ...
piv_obj_to_matrix(pivobj_CDH_2_mg_blured_stripes_thr8{i});
x_c=CDH_2_mg_center.xs(i);
y_c=CDH_2_mg_center.ys(i);
cond_core=(pivobj_CDH_2_mg_blured_stripes_thr8{i}.xs-x_c).^2+...
(pivobj_CDH_2_mg_blured_stripes_thr8{i}.ys-y_c).^2<=R_core^2;
vxs_core_all_t_CDH_2_mg_blured_stripes_thr8{i}=...
pivobj_CDH_2_mg_blured_stripes_thr8{i}.vxs(...
cond_core);
vys_core_all_t_CDH_2_mg_blured_stripes_thr8{i}=...
pivobj_CDH_2_mg_blured_stripes_thr8{i}.vys(...
cond_core);
cond_bulk=(pivobj_CDH_2_mg_blured_stripes_thr8{i}.xs-x_c).^2+...
(pivobj_CDH_2_mg_blured_stripes_thr8{i}.ys-y_c).^2<=R_bulk_2^2 & ...
(pivobj_CDH_2_mg_blured_stripes_thr8{i}.xs-x_c).^2+...
(pivobj_CDH_2_mg_blured_stripes_thr8{i}.ys-y_c).^2>R_bulk_1^2;
vxs_bulk_all_t_CDH_2_mg_blured_stripes_thr8{i}=...
pivobj_CDH_2_mg_blured_stripes_thr8{i}.vxs(...
cond_bulk);
vys_bulk_all_t_CDH_2_mg_blured_stripes_thr8{i}=...
pivobj_CDH_2_mg_blured_stripes_thr8{i}.vys(...
cond_bulk);
cond_border=(pivobj_CDH_2_mg_blured_stripes_thr8{i}.xs-x_c).^2+...
(pivobj_CDH_2_mg_blured_stripes_thr8{i}.ys-y_c).^2>R_border_1^2 & ...
(pivobj_CDH_2_mg_blured_stripes_thr8{i}.xs-x_c).^2+...
(pivobj_CDH_2_mg_blured_stripes_thr8{i}.ys-y_c).^2<=R_border_2^2;
vxs_border_all_t_CDH_2_mg_blured_stripes_thr8{i}=...
pivobj_CDH_2_mg_blured_stripes_thr8{i}.vxs(...
cond_border);
vys_border_all_t_CDH_2_mg_blured_stripes_thr8{i}=...
pivobj_CDH_2_mg_blured_stripes_thr8{i}.vys(...
cond_border);
figure
fh=sqrt(vxs_core_all_t_CDH_2_mg_blured_stripes_thr8{i}.^2+...
vys_core_all_t_CDH_2_mg_blured_stripes_thr8{i}.^2);
h=histogram(fh(~isnan(fh)),...
linspace(0,25,100),'Normalization','pdf');
write_2_column_table(['pdf_vabs_core_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
h.BinEdges(1:end-1),h.Values)
write_1_column_table(['all_vabs_core_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
fh(~isnan(fh)))
hold on
fh=sqrt(vxs_bulk_all_t_CDH_2_mg_blured_stripes_thr8{i}.^2+...
vys_bulk_all_t_CDH_2_mg_blured_stripes_thr8{i}.^2);
h=histogram(fh(~isnan(fh)),...
linspace(0,25,100),'Normalization','pdf');
write_2_column_table(['pdf_vabs_bulk_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
h.BinEdges(1:end-1),h.Values)
write_1_column_table(['all_vabs_bulk_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
fh(~isnan(fh)))
hold on
fh=sqrt(vxs_border_all_t_CDH_2_mg_blured_stripes_thr8{i}.^2+...
vys_border_all_t_CDH_2_mg_blured_stripes_thr8{i}.^2);
h=histogram(fh(~isnan(fh)),...
linspace(0,25,100),'Normalization','pdf');
write_2_column_table(['pdf_vabs_border_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
h.BinEdges(1:end-1),h.Values)
write_1_column_table(['all_vabs_border_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
fh(~isnan(fh)))
vort_core_CDH_2_mg_blured_stripes_thr8{i}=pivCURLz_all_CDH_2mg_blured_thr(cond_core); %pivobj_CDH_2_mg_blured{i}.loaded_vort
vort_bulk_CDH_2_mg_blured_stripes_thr8{i}=pivCURLz_all_CDH_2mg_blured_thr(cond_bulk); % pivobj_CDH_2_mg_blured{i}.loaded_vort
vort_border_CDH_2_mg_blured_stripes_thr8{i}=pivCURLz_all_CDH_2mg_blured_thr(cond_border); %pivobj_CDH_2_mg_blured{i}.loaded_vort
figure
fh=vort_core_CDH_2_mg_blured_stripes_thr8{i};
h=histogram(fh(~isnan(fh)),...
linspace(-1.5,1.5,100),'Normalization','pdf');
write_2_column_table(['pdf_vort_core_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
h.BinEdges(1:end-1),h.Values)
write_1_column_table(['all_vort_core_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
fh(~isnan(fh)))
hold on
fh=vort_bulk_CDH_2_mg_blured_stripes_thr8{i};
h=histogram(fh(~isnan(fh)),...
linspace(-1.5,1.5,100),'Normalization','pdf');
write_2_column_table(['pdf_vort_bulk_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
h.BinEdges(1:end-1),h.Values)
write_1_column_table(['all_vort_bulk_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
fh(~isnan(fh)))
hold on
fh=vort_border_CDH_2_mg_blured_stripes_thr8{i};
h=histogram(fh(~isnan(fh)),...
linspace(-1.5,1.5,100),'Normalization','pdf');
write_2_column_table(['pdf_vort_border_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
h.BinEdges(1:end-1),h.Values)
write_1_column_table(['all_vort_border_stripes_thr8_bluredCDH_2_mg_' num2str(i) '.dat'],...
fh(~isnan(fh)))
R_positions=sqrt((pivobj_CDH_2_mg_blured_stripes_thr8{i}.xs-x_c).^2 + ...
(pivobj_CDH_2_mg_blured_stripes_thr8{i}.ys-y_c).^2);
absv_all=sqrt(pivobj_CDH_2_mg_blured_stripes_thr8{i}.vxs.^2+pivobj_CDH_2_mg_blured_stripes_thr8{i}.vys.^2);
abscurlz_all=pivCURLz_all_CDH_2mg_blured_thr;
absdiv_all=pivDIVall_CDH_2mg_blured_thr;
for j=1:num_prof_points
cond_RdR=(R_positions<(j*dR)) & (R_positions>=((j-1)*dR));
av_vel_profile_bluredCDH_2_stripes_thr8{i}(j)=nanmean(absv_all(cond_RdR));
av_curlz_profile_bluredCDH_2_stripes_thr8{i}(j)=nanmean(abs(abscurlz_all(cond_RdR)));
av_div_profile_bluredCDH_2_stripes_thr8{i}(j)=nanmean((absdiv_all(cond_RdR)));
end
figure;
plot((1:num_prof_points)*dR,av_vel_profile_bluredCDH_2_stripes_thr8{i})
hold on
write_2_column_table(['velocity_profile_stripes_thr8_bluredCDH_2_mg_set_'...
num2str(i) '.dat' ], (1:num_prof_points)*dR ,...
av_vel_profile_bluredCDH_2_stripes_thr8{i})
xlabel('r')
ylabel('mean v')
legend('Location','best')
title('CDH 2 mg')
set(gca,'FontSize', 14)
figure
plot((1:num_prof_points)*dR,av_curlz_profile_bluredCDH_2_stripes_thr8{i},...
'DisplayName',['set ' num2str(i)])
hold on
write_2_column_table(['blured_absvort_profile_stripes_thr8_bluredCDH_2_mg_set_'...
num2str(i) '.dat' ], (1:num_prof_points)*dR ,...
av_curlz_profile_bluredCDH_2_stripes_thr8{i})
figure
plot((1:num_prof_points)*dR,av_div_profile_bluredCDH_2_stripes_thr8{i},...
'DisplayName',['set ' num2str(i)])
hold on
write_2_column_table(['blured_div_profile_stripes_thr8_bluredCDH_2_mg_set_'...
num2str(i) '.dat' ], (1:num_prof_points)*dR ,...
av_div_profile_bluredCDH_2_stripes_thr8{i})
end