README plus other functionalities.

CODE/DEMOS/demoLoadXLSandPlot.m

@@ -12,6 +12,9 @@
 mcrsght_info('Loaded table (first 10 columns):');
 disp(dataTable(1:10,:));
 
+controlplot = dataStructure.controlplot;
+mutantplot  = dataStructure.mutantplot;
+
 preaxis = [-27 18 -12 13];
 figure(2)
 clf;

CODE/DEMOS/demoStatisticalAnalysis.m

@@ -0,0 +1,55 @@
+clc;
+mcrsght_info('LOAD CONTACT EVENTS FROM SAVED EXPERIMENT - BRIEF ANALYSIS.');
+mcrsght_info('This demo uses the experiment in [./DATA/ctrlvshot3/demo2_*],');
+mcrsght_info('and performs a simple T-test and boxplots. ');
+
+basefilename = fullfile(MACROHOME_,'DATA','ctrlvshot3');
+dataStructure = load(fullfile(basefilename, 'demo2_angleChanges.mat'));
+dataTable = readtable(fullfile(basefilename, 'demo2_angleChanges.xlsx'));
+
+mcrsght_info('Loaded variables:');
+disp(dataStructure);
+
+controltrackfeatures = dataStructure.controltrackfeatures;
+mutanttrackfeatures   = dataStructure.mutanttrackfeatures;
+setnames = {dataStructure.generalinfocontrol(1).typeExperiment ...
+            dataStructure.generalinfomutant(1).typeExperiment};
+
+
+
+[boxdata,boxgroups] = getBoxplotComparisonData(controltrackfeatures, mutanttrackfeatures);
+
+subplot(141)
+boxplot(boxdata.clumpsize, boxgroups);
+ylabel('clumpsize');
+title('Boxplot example - 1');
+
+subplot(142)
+boxplot(boxdata.thx, boxgroups);
+ylabel('anglechange');
+title('Boxplot example - 2');
+
+subplot(143)
+boxplot(abs(boxdata.thx), boxgroups);
+ylabel('abs(anglechange)');
+title('Boxplot example - 3');
+
+subplot(144)
+hold on;
+for ix=1:2
+    scatter(boxdata.clumpsize(boxgroups==ix), abs(boxdata.thx(boxgroups==ix)), 110);
+end
+legend(setnames);
+xlabel('clumpsize');
+ylabel('abs(angle change)');
+title('Scatterplot example');
+
+set(gcf, 'Position', [560   579   983   369]);
+
+[M, SD, H, P] = compareAngleChanges(controltrackfeatures, mutanttrackfeatures, setnames);
+mcrsght_info(sprintf('SET: [%s] MEAN(STDev) = %2.2f(%2.2f) ', ...
+                setnames{1}, M.(setnames{1}), SD.(setnames{1})), 'RESULTS');
+mcrsght_info(sprintf('SET: [%s] MEAN(STDev) = %2.2f(%2.2f) ', ...
+                setnames{2}, M.(setnames{2}), SD.(setnames{2})), 'RESULTS');
+mcrsght_info(sprintf('TESTS: T-test p-value = %2.2f ', P.ttest), 'RESULTS');
+mcrsght_info(sprintf('TESTS: Wilcoxon p-value = %2.2f ', P.wilcoxon), 'RESULTS');

CODE/compareAngleChanges.m

@@ -0,0 +1,65 @@
+function [M, SD, H, P] = compareAngleChanges(trackfeatures_set1, trackfeatures_set2, setnames, absbool)
+%
+
+if nargin < 3
+    setnames = {'set1', 'set2'};
+    absbool = true;
+elseif nargin < 4
+    absbool = true;
+end
+
+if absbool
+    mcrsght_info('ABS(Angle)');
+else
+    mcrsght_info('Angles unchanged');
+end
+
+angleContact = vertcat(trackfeatures_set1.thx);
+angleNoContact = vertcat(trackfeatures_set2.thx);
+
+
+if absbool
+    angleContact = abs(angleContact);
+    angleNoContact = abs(angleNoContact);
+end
+
+m = [mean(angleContact) mean(angleNoContact)];
+sd = [std(angleContact) std(angleNoContact)];
+
+[pwill, hwill] = ranksum(angleContact, angleNoContact);
+[httest, pttest] = ttest2(angleContact, angleNoContact);
+
+if hwill==1
+    rejwill = 'reject';
+else
+    rejwill = sprintf('nope\t');
+end
+if httest==1
+    rejttest = 'reject';
+else
+    rejttest = sprintf('nope\t');
+end
+
+M.(setnames{1}) = m(1);
+M.(setnames{2}) = m(2);
+
+SD.(setnames{1}) = sd(1);
+SD.(setnames{2}) = sd(2);
+
+H.ttest = httest;
+H.wilcoxon = hwill;
+
+P.ttest = pttest;
+P.wilcoxon = pwill;
+
+
+if nargout == 0
+    mcrsght_info(sprintf('   & With cell-cell  &  NO contact  &     WILLCOXON         &     T-TEST           &'));
+    mcrsght_info(sprintf('mean (std)    &  mean (std)  & p-value & Can reject? & p-value & Can reject? &'));
+
+    mcrsght_info(sprintf('& %3.2f (%2.2f)  & %3.2f (%2.2f)  &  %2.2f   & %s  &   %2.2f  & %s  &', ...
+        m(1), sd(1), m(2), sd(2), pwill, rejwill, pttest, rejttest));
+
+end
+
+

CODE/getBoxplotComparisonData.m

@@ -0,0 +1,19 @@
+function [boxdata, boxgroups] = getBoxplotComparisonData(varargin)
+% GET DATA FOR BOXPLOTS AND STATISTICAL ANALYSIS.
+%
+
+numGroups = length(varargin);
+fnames = fieldnames(varargin{1});
+
+boxgroups = [];
+for ix=1:length(fnames)
+    Tab = [];
+    for jx=1:numGroups
+        thisVector = vertcat(varargin{jx}.(fnames{ix}));
+        Tab = [Tab; thisVector];
+        if ix==1
+            boxgroups = [boxgroups; jx.*ones(size(thisVector))];
+        end
+    end
+    boxdata.(fnames{ix}) = Tab;
+end

README.md

@@ -4,64 +4,60 @@ This code is based on the [phagosight](https://github.com/phagosight/phagosight)
 software, but modules for the analysis of overlapping cells within a video sequence
 have been added.
 
-## Quick start
-A brief summary to start the analysis as quickly as possible.
-
-### Installation
-To clone this repository **and its dependencies (phagosight)** use the following 
-command: 
+## Installation
+To clone this repository use the following command:
 ```bash
-git clone --recursive https://github.com/alonsoJASL/macrosight/ 
+git clone https://github.com/alonsoJASL/macrosight/
 ```
-This will allow @phagosight and macrosight to be pulled into nested folders. To 
-configure the paths automatically, **inside Matlab** Run the command `configureMacrosight`.
 
-### Requirements of the data
-The macrophages dataset need to be in individual files, with the following naming 
-convention: 
+To configure the paths automatically, **inside Matlab**, run the command
+`configureMacrosight`. If you have @phagosight, then the configuration will
+walk you through adding it to your path. Otherwise, you can choose not to use
+it.
+
+## Quick start
+The best way to see Macrosight's functionalities is through the demos. In
+Matlab run
 ```Matlab
-/path/to/data/MACROSN/T000ix.tif
+macrosight_demo
+```
+to get a list of ready-made examples of the software functionalities:
+```
+macrosight_demo
+[MACROSIGHT_DEMOS] Select the demo from the list:
+[1] Select contact events - save to xls.
+[2] Load from saved data - plot results
+[3] Load from saved data - statistical analysis
+[9] Demo tidy function
+[C] Cancel
+Your choice [default=1]:
 ```
-where `N` corresponds to the nth experiment and  `ix` correspond to each image's 
-identifier.
-
-Functionalities will soon be included to prepare the data automatically.
 
-### Quick start guide
-Macrosight takes images storede in a hard drive, and saves the output to other
-folders following a specific naming scheme. 
+### Quick start using phagosight functionalies (from scratch)
+Tracking needs PhagoSight, clone it with the
+command:
+```bash
+git clone https://github.com/phagosight/phagosight/
+```
+and then in Matlab run `configureMacrosight`.
 
-For **segmentation**, see the file [`preinit_segmentation.m`](../preinit_segmentation.m).
+Macrosight takes images stored in a hard drive, and saves the output to other
+folders following a specific naming scheme. For **segmentation**, see the file [`preinit_segmentation.m`](./CODE/pre-release-scripts/preinit_segmentation.m).
 This script arranges the data into the cooresponding output folders
 + `_data_Ha`
 + `_data_Re`
-+ `_data_La
++ `_data_La`
 
-**Tracking** and inclusion of **clump information**, is done in the initialisation
-file: [`initscript.m`](../initscript.m). The file allows the user to select an 
-experiment and continue on a previously loaded dataset.
+**Tracking** and inclusion of **clump information**, is done with the setup
+function: [`setupInitialStructures.m`](./CODE/setupInitialStructures.m).
+The function allows the user to select an experiment and continue on a
+previously loaded dataset.
+
+```Matlab
+[tablenet, clumptracktable, clumpidcodes, ~] = setupInitialStructures();
+```
 
 ## Troubleshooting and questions
-Macrosight is an ongoing project at an early stage. We welcome all feedback and 
-comments in the [issues](https://github.com/alonsoJASL/macrosight/issues) 
+Macrosight is an ongoing project at an early stage. We welcome all feedback and
+comments in the [issues](https://github.com/alonsoJASL/macrosight/issues)
 page.
-
-## Log files
-The log files kept for this package are not written for a full explanation, but
-rather as a way to keep track of the developments made. So if there is some
-problem with it, just ask me! The log files can be read in the following order:
-+ [Shape analysis log](./md-logs/shapeanalysis-log.md)
-+ [Single cell following log](./md-logs/shapeanalysis-singlecell.md), a
-previous step from   __shape evolution__.
-+ [Shape evolution](./md-logs/shapeevolution-log.md) **CURRENTLY under development**. 
-Some of the images present can be hard to see, but the MATLAB fig or EPS files are 
-present in the [`figs` folder](./figs).
-+ (Original development, then switched approach to **shape evolution**)
-[SOM shape evolution log](./md-logs/shapeandsom-log.md). This is not finalised.
-
-Also, please notice that this research is ongoing, so bugs are likely to appear. 
-Some of the functions might not be present, because they are part of another package
-that has not been uploaded. 
-If you are thinking of using our code, please feel free to submit any issues to the 
-[issues page](https://github.com/alonsoJASL/macrosight/issues), so that small bugs are 
-dealt with. 

configureMacrosight.m

@@ -34,31 +34,42 @@
         fprintf('\t%d: %s\n', ix, b_{ix});
     end
     folderchoice_ = input(sprintf(...
-        '\nChoose the folder containing PhagoSight \n%s\n%s\n%s:__', ...
-        '0 := it is not found', '1 := default', 'Your choice'));
+        '\nChoose the folder containing PhagoSight \n%s\n%s\n%s\n%s:__', ...
+        '0 := it is not found', '1 := default', 'C := not using phagosight', 'Your choice'),'s');
 end
 
 if isempty(folderchoice_)
-    folderchoice_ = 1;
+    folderchoice_ = '1';
 end
 
-if folderchoice_== 0 % not found
-    disp('Pick the location of PhagoSight');
-    pause(0.5);
-    PHAGOHOME_ = uigetdir(MACROHOME_,'Pick a directory');
+if strcmpi(folderchoice_, 'c')
+    mcrsght_info('Not using PhagoSight - some features might not work.', 'ATTENTION');
+    fprintf('Adding the following to the MATLAB path:\n%s\n%s\n', ...
+        fullfile(MACROHOME_, 'CODE'), ...
+        fullfile(MACROHOME_, 'CODE', 'DEMOS'));
+
+    addpath(fullfile(MACROHOME_, 'CODE'), ...
+        fullfile(MACROHOME_, 'CODE', 'DEMOS'));
 else
-    PHAGOHOME_ = b_{folderchoice_};
+
+    if strcmpi(folderchoice_,'0') % not found
+        disp('Pick the location of PhagoSight');
+        pause(0.5);
+        PHAGOHOME_ = uigetdir(MACROHOME_,'Pick a directory');
+    else
+        PHAGOHOME_ = b_{str2num(folderchoice_)};
+    end
+    fprintf('Adding the following to the MATLAB path:\n%s\n%s\n%s\n', ...
+        fullfile(PHAGOHOME_, 'CODE'), ...
+        fullfile(MACROHOME_, 'CODE'), ...
+        fullfile(MACROHOME_, 'CODE', 'DEMOS'));
+
+    addpath(fullfile(PHAGOHOME_, 'CODE'), ...
+        fullfile(MACROHOME_, 'CODE'), ...
+        fullfile(MACROHOME_, 'CODE', 'DEMOS'));
 end
 
 
-fprintf('Adding the following to the MATLAB path:\n%s\n%s\n%s\n', ...
-    fullfile(PHAGOHOME_, 'CODE'), ...
-    fullfile(MACROHOME_, 'CODE'), ...
-    fullfile(MACROHOME_, 'CODE', 'DEMOS'));
-
-addpath(fullfile(PHAGOHOME_, 'CODE'), ...
-        fullfile(MACROHOME_, 'CODE'), ...
-        fullfile(MACROHOME_, 'CODE', 'DEMOS'));
 
 clear a_ b_ folderchoice_ ix test_;
 

macrosight_demo.m

@@ -1,7 +1,10 @@
 mcrsght_info('Select the demo from the list:', 'MACROSIGHT_DEMOS');
 
 mcrsght_info('Select contact events - save to xls.', '1');
-mcrsght_info('Load from xls - plot results','2');
+mcrsght_info('Load from saved data - plot results','2');
+mcrsght_info('Load from saved data - statistical analysis','3');
+mcrsght_info('Demo tidy function','9');
+mcrsght_info('Cancel','C');
 
 demoinput_ = input('Your choice [default=1]: ', 's');
 if isempty(demoinput_)
@@ -13,5 +16,11 @@
         demoSelectContactSingle; 
     case '2'
         demoLoadXLSandPlot;
+    case '3'
+        demoStatisticalAnalysis;
+    case '9'
+        tidy;
+    otherwise 
+        mcrsght_info('Cancelled demo.');
 end
-
+clear demoinput_;