Restored initial version without data directory

source/A_control.m → A_control.m

@@ -146,7 +146,7 @@
 
 elseif task==18
     clear('btn','button','task')
-    A_save_res_inter; 
+    A_save_res; 
 
 elseif task==19
     clear('btn','button','task')

A_load_result.m

@@ -0,0 +1,27 @@
+close all
+clear
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+try
+[pathname,dirname] = uigetfile('Res-*.mat');
+fullpath = fullfile(dirname,pathname);
+dirnamen=dirname;
+load(fullpath);
+testname=pathname;
+dirname1=dirnamen;
+dirname2=dirnamen;
+exnameo1= strrep(exname1,'-','_');
+exnameo2= strrep(exname2,'-','_');
+fullpath1=[dirname1,exnameo1];
+fullpath2=[dirname2,exnameo2];
+
+
+msgbox('Current results are successfully loaded')
+ A_plot_data_label;
+clear('fullpath','pathname','dirnamen','dirname')
+clear('che','tekst')
+clear('exnameo1','exnameo2')
+catch
+    clc
+    msgbox('Fullpath is not correct. Please load new data')
+    A_start
+end   

source/A_menu.m → A_menu.m

@@ -24,9 +24,9 @@
 'IMPORT DATA from Excel',...
 'EXIT'};                                %task 20
 
-
+clc
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-options.Interpreter = 'latex';
+options.Interpreter = 'tex';
 figure(2000)
 whitebg([0,0,50]/255) % background color
 close figure 2000

source/A_plot_data_label.m → A_plot_data_label.m

@@ -14,11 +14,8 @@
       A_start;  
     end
 
-if exist('para_nr','var')==1
-    tt=num2str(para_nr);
-else
-    tt='new pair';
-end
+
+
 
 
 if exist('dat2','var')==1
@@ -32,12 +29,10 @@
                   'Colormap'    ,[], ...
                   'MenuBar'     ,'none',...
                   'ToolBar' 	,'none', ...
-                  'Position',[scrsz(3)/5 scrsz(4)/1.25 scrsz(4)/0.8 scrsz(4)/7.25]);
+                  'Position',[scrsz(3)/5 scrsz(4)/1.18 scrsz(4)/0.8 scrsz(4)/10.25]);
 whitebg(get(gcf,'color'));
 text(0.01,0.75,['Sample 1:   ',exname1,': ',num2str(N1),' points'],'Fontsize',12,'Fontweight','bold')
-text(0.01,0.45,['Sample 2:   ',exname2,': ',num2str(N2),' points'],'Fontsize',12,'Fontweight','bold')
-text(0.01,0.18,['Number of pair :   ',tt],'Fontsize',12,'Fontweight','bold')
-
+text(0.01,0.35,['Sample 2:   ',exname2,': ',num2str(N2),' points'],'Fontsize',12,'Fontweight','bold')
 ax = gca;
 
 

source/A_random_generator_neu.m → A_random_generator_neu.m

@@ -13,7 +13,7 @@
 
 sigma_factor=3.0;
 poiss_factor=1.0;
-stop_random_noise;
+min_element=15;
 poiss_met=1;
 norm_pdf1=0;
 
@@ -164,12 +164,12 @@
 UK=UK-KL;
 
 if UK>0
+    stop_random_noise;
     urr=[];
     for kk=1:UK
        if noi==1
        urr(kk,:) = mddd+deltaddd.*rand(1,3);
        elseif noi==0
-
        urr(kk,:) = mddd+deltaddd.*0;     
        end  
     end
@@ -228,6 +228,7 @@
 
 
 
+
 clear('Zori','cluster_main','SYR','Mddd','mddd', 'rrr','size_rys',...
     'deltaddd', 'nnn', 'nn00', 'de', 'sss', 'dd00','ktrys','Nmaxor',...
     'ep' ,'KL','wu', 'r00', 'muhat','sigmahat','UK', 'urr', 'kk', 'i', 'k', 'j','clind','ii','ktrys',...

source/A_save_res.m → A_save_res.m

@@ -23,15 +23,16 @@
 elseif contains(exname1,'blue')==1
     te1=['blue',extractAfter(exname1,'blue')];
 else
-    te1=exname1(1:3);
+    te1='';
 end   
 if contains(exname2,'red')==1
     te2=['red',extractAfter(exname2,'red')];
 elseif contains(exname2,'blue')==1
     te2=['blue',extractAfter(exname2,'blue')];
 else
-    te2=exname2(1:3);
+    te2='';
 end   
+answer_pair_nr;
 if strcmp(te1,te2)==0
 te = [num2str(para_nr),'-',te1,'-',te2] ;
 else

source/A_start.m → A_start.m

@@ -1,6 +1,6 @@
 
 
-%CALM Version 4.2  (2-sample Comparative Analysis of 3D Localisation Microscopy data) 
+%CALM Version 2.1  (2-sample Comparative Analysis of 3D Localisation Microscopy data) 
 %is an analysis pipeline, which organizes localisation microscopy data into 
 %clusters of different dimensions and calculated the samples’ statistical parameters
 %using various numerical methods.
@@ -45,26 +45,26 @@
 % This code may be freely used and distributed, so long as it maintains this copyright line
 
 
-
+clc
 try
     close(hh)
     clear('hh')
 catch
     clear('hh')
 end
 
-            %try
+            try
 A_menu;
 A_control
 clear('task')
 A_start;
-           %catch
-             %clc
-             % disp('The program was aborted by the user')
-            %  pause(0.01)
-             % user_stops;
+            catch
+                clc
+                disp('The program was aborted by the user')
+                pause(0.01)
+                user_stops;
 
-         %  end
+            end
 
 
 

CALM.m

@@ -1,9 +1,11 @@
-%CALM Version 4.2  (2-sample Comparative Analysis of 3D Localisation Microscopy data) 
+
+
+%CALM Version 2.1  (2-sample Comparative Analysis of 3D Localisation Microscopy data) 
 %is an analysis pipeline, which organizes localisation microscopy data into 
 %clusters of different dimensions and calculated the samples’ statistical parameters
 %using various numerical methods.
 %
-%   CALM Version 4.2 is the prototype software platform that allows a comparative analysis of 
+%   CALM Version 2.1 is the prototype software platform that allows a comparative analysis of 
 %   3D localisation microscopy data representing protein distributions in two biological samples. 
 %   The platform contains published functions (see comments in the function) 
 %   as well as many own functions and scripts (without comments).
@@ -37,21 +39,23 @@
 %  In the absence of these columns they will be automatically generated 
 %  with default values typical for this type of nanoscopic samples.
 %
-% Copyright 2018 - 2021 Jaroslaw Jacak, 
+%
+%
+% Copyright 2018 Jaroslaw Jacak, 
 % Medical Engineering Dept. Upper Austria University od Applied Sciences, Linz, Austria
 % This code may be freely used and distributed, so long as it maintains this copyright line
 
-addpath('source')
 
-Figure_start;
-clear('scrsz','T')
-try
-    A_start;
-catch
-    clc
+
+  Figure_start;
+  clear('scrsz','T')
+ try
+   A_start;
+ catch
+  clc
     disp('The program was aborted by the user')
     %user_stops
-end
+ end
 
 
 

source/DBSCAN_neu.m → DBSCAN_neu.m

@@ -10,9 +10,8 @@
 % 
 % alpha coefficient for neighborhood radius(=1)
 % NP number of neighbors (min 5)
-% NPP neigbors number for neighbors (min 4)
+% NPP neifgbors number for neighbors (min 4)
 % pos,  points in original order
-% N Number of points 
 
 %%%%%%%%%%%%%%%%%%%%%%% data init %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
@@ -22,15 +21,15 @@
 %disp('Primary cluster generation. Please wait a few minutes')
 
 
-NRAD=alpha*avg_min_dist ;                       %%% minimal raius of neighborhood
+NRAD=alpha*avg_min_dist ;                       %%% minimal raius oh neighborhood
 cl(1:N,1)=0;                                    % cluster
 al(1:N,1)=0;                                    % analyse marker
 C=0;                                  
 %tic
 
 %%%%%%%%%%%%%%%%%%%% primary cluster finding %%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
- %kontr=round(0.1*N);                                    % current cluster number
+ %kontr=3000;                                         % current cluster number
  %jab=1;
 
 for i=1:N

source/Data_Load_1.m → Data_Load_1.m

@@ -2,18 +2,16 @@
 close all
 clear
 %%%%%%%%%%%%%%%%%%%%%%%%% open file %%%%%%%%%%%%%%%%%%%%%%%%%%%
-[pathname,dirname] = uigetfile('../*.mat');
+[pathname,dirname] = uigetfile('*.mat');
 fullpath = fullfile(dirname,pathname);
 fullpath1=fullpath;
 dirname1=dirname;
-pathname1=pathname;
-
 load(fullpath);
 exname=pathname;
+
 exname = strrep(exname,'_','-');
 exname1 = strrep(exname,'.mat','');
 
-
 clear('fullpath','datacell','dirname',  'pathname')
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 data_test= exist('par','var');

source/Data_Load_2.m → Data_Load_2.m

@@ -2,12 +2,10 @@
 
 
 %%%%%%%%%%%%%%%%%%%%%%%%% open file %%%%%%%%%%%%%%%%%%%%%%%%%%%
-[pathname,dirname] = uigetfile('../*.mat');
+[pathname,dirname] = uigetfile('*.mat');
 fullpath = fullfile(dirname,pathname);
 fullpath2=fullpath;
 dirname2=dirname;
-pathname2=pathname;
-
 load(fullpath);
 exname=pathname;
 exname = strrep(exname,'_','-');

source/E_read.m → E_read.m

@@ -3,7 +3,7 @@
 clear
 %%%%%%%%%%%%%%%%%%%%%%%%% open file %%%%%%%%%%%%%%%%%%%%%%%%%%%
 try
-[pathname,dirname] = uigetfile('..\*.x*');
+[pathname,dirname] = uigetfile('*.x*');
 fullpath = fullfile(dirname,pathname);
 par= importdata(fullpath);  
 catch

source/Figure_start.m → Figure_start.m

@@ -5,8 +5,8 @@
 figure ( 'WindowStyle', 'normal', ...  
                   'Visible'     ,'on', ...
                   'NumberTitle' ,'off', ...
-                  'Name'        ,'2CALM V4.1', ...
-                  'Resize'      ,'on', ...
+                  'Name'        ,'2CALM V2', ...
+                  'Resize'      ,'off', ...
                   'Colormap'    ,[], ...
                   'MenuBar'     ,'none',...
                   'ToolBar' 	,'none',...

README.md

@@ -1,34 +1,47 @@
 # 2CALM
 
-CALM Version 4.2 (2-sample Comparative Analysis of 3D Localisation Microscopy data) is an analysis pipeline, which organizes localisation microscopy data into clusters of different dimensions and calculated the samples’ statistical parameters using various numerical methods.
-
-CALM Version 4.2 is the prototype software platform that allows a comparative analysis of 3D localisation microscopy data representing e.g. protein distributions in two biological samples. The CALM 4.2 system includes a collection of functions and scripts for handling individual menu items. The system should be unpacked together with the main CALM 4.2 directory and subdirectories (the subdirectories can be freely extended, e.g. for individual experiments). 
-
-The system starts in the Matlab (min Version R2018) with the `CALM.m` command.
-
-In this prototype system, the input data structure is limited to specified matlab format. Data set must be of type structure array named `par`. The structure must contain the fields:
-   * `par.pkmatrix` – array of numerical data with row-measurements and columns- data coordinates.
-   * `par.pkdesc` - contains two cells par.pkdesc.desc, and par.pkdesc.units:
-   * `par.pkdesc.desc` - gives a description of the pkmatrix-columns line 
-   * with at least the following string variables: `frame`; `x`; `y`; `z`; `pa`; `paz`; `intensity` where `pa` is the position accuracy of xy localization and `paz` is position accuracy of localization on z-axis. `frame` is frame number.
-   * par.pkdesc.units contains a description  of the units of measure for each column in string format.
+CALM Version 2.1  (2-sample Comparative Analysis of 3D Localisation Microscopy data) 
+is an analysis pipeline, which organizes localisation microscopy data into 
+clusters of different dimensions and calculated the samples’ statistical parameters
+using various numerical methods.
+
+CALM Version 2.1 is the prototype software platform that allows a comparative analysis of 
+3D localisation microscopy data representing protein distributions in two biological samples. 
+The platform contains published functions (see comments in the function) 
+as well as many own functions and scripts (without comments).
+
+In this prototype system, the input data structure is limited to specified matlab format.
+Data set must be of type structure array named "par". The structure must contain 
+the fields:
+   par.pkmatrix – array of numerical data with row-measurements and
+   columns- data coordinates.
+   par.pkdesc - contains two cells par.pkdesc.desc, and par.pkdesc.units:
+   par.pkdesc.desc - gives a description of the pkmatrix-columns line 
+   with at least the following string variables:
+   "frame"; "x"; "y"; "z"; "pa"; "paz"; "intensity"  where "pa" is the position accuracy 
+   of xy localization and 
+   "paz"
+    is position accuracy of localization on z-axis. "frame" is frame number.
+   par.pkdesc.units contains a description  of the units of measure 
+   for each column in string format.
 
-## IMPORT DATA FROM EXCEL
+IMPORT DATA FROM EXCEL
    In order to enable analysis of data in another format, the system has an interface to Excel
    that imports and transfers Excel data to the Matlab format described above.  
    Excel data spreadsheet  must be column-oriented and  must have at least 3 columns 
-   (3D point localizations) with column headers `x`, `y`, `z`.
-   If possible, the following additional columns should contain:
-   * position accuracy (in nm) in xy with header `pa`
-   * position accuracy (in nm) along the axis z with header `paz`
-   * intensity of the point with the header `intensity`
-   * the frame number with the `frame` header
+   (3D point localizations) with column headers "x", "y", "z".
+   If possible, the following additional columns should contain :
+   - position accuracy (in nm) in xy with header "pa",
+   - position accuracy (in nm) along the axis z with header "paz",
+   - intensity of the point with the header "intensity",
+   - and the frame number with the "frame" header.
 
-   In the absence of these columns they will be automatically generated with default values typical for this type of nanoscopic samples.
+  In the absence of these columns they will be automatically generated 
+  with default values typical for this type of nanoscopic samples.
 
 
 # License
-Copyright 2018 - 2021 Jaroslaw Jacak, 
+Copyright 2018 - 2020 Jaroslaw Jacak, 
 Medical Engineering Dept. Upper Austria University od Applied Sciences, Linz, Austria
 This code may be freely used and distributed, so long as it maintains this copyright line
 

source/RipleysK3D.m → RipleysK3D.m

@@ -16,7 +16,6 @@
 genau=1;
 % genau=0 volumen of sample as vol bounding box
 % genau=1 volumen of sample as vol convexhull
-
 if nargin<4
     method=1; 
 end
@@ -68,9 +67,13 @@
 else
 lambda = N/((box(2)-box(1))*(box(4)-box(3))*(box(6)-box(5)));
 end
-lambda=1;
 K = K/lambda;
 
+
+
+
+
+
 end