Add example script Example_SPT_movie.

Author: MJWester1

MATLAB/+smi_helpers/versionSMITE.m

@@ -17,5 +17,6 @@
    %version = '1.1.6';   % pearsonCorrCoef added to smi_stats
    %version = '1.2.0';   % cleanup of PairAnalysis class; added Manders' coeffs
    %version = '1.2.1';   % For 2-color, select ROIs from a Gaussian image
-   version = '1.2.2';   % made HopTestPts and HopTests user adjustable
+   %version = '1.2.2';   % made HopTestPts and HopTests user adjustable
+   version = '1.2.3';   % add example script Example_SPT_movie
 end

MATLAB/examples/Example_Publish_SMF.m

@@ -0,0 +1,54 @@
+% Produce a movie from SPT results.
+%
+TrackingResults = 'NEEDS_TO_BE_SET!';
+RawData = 'NEEDS_TO_BE_SET!'
+
+% Load SMITE processed tracking results: SMF, SMD, TR.
+load(TrackingResults);
+% Load raw blinking data.
+load(RawData);
+
+%sliceViewer(Channel_1);
+
+GM = smi_vis.GenerateMovies();
+GM.SMF = SMF;
+GM.SMD = SMD;
+GM.TR  = TR;
+GM.RawData = Channel_1;
+
+% Set some parameters; see smi_vis.GenerateMovies.prepDefaults for a full list,
+%
+% Place the indicated marker on each localization given in GM.SMD
+%GM.Params.SMDMarker = 'x';
+% Maximum number of points of a given trajectory that will be plotted. 
+GM.Params.MaxTrajLength = 5;
+% Choose a ROI to examine (default is entire image):
+%raw_size = size(GM.RawData);
+%GM.Params.XPixels = [0, raw_size(1) - 1];
+%GM.Params.YPixels = [0, raw_size(2) - 1];
+GM.Params.XPixels = [64, 127];
+GM.Params.YPixels = [64, 127];
+
+%sliceViewer(Channel_1);
+
+GM = smi_vis.GenerateMovies();
+GM.SMF = SMF;
+GM.SMD = SMD;
+GM.TR  = TR;
+GM.RawData = Channel_1;
+% Set some parameters; see smi_vis,GenerateMovies.prepDefaults for a full list,
+%
+% Place the indicated marker on each localization given in GM.SMD
+%GM.Params.SMDMarker = 'x';
+% Maximum number of points of a given trajectory that will be plotted. 
+GM.Params.MaxTrajLength = 5;
+% Choose a ROI to examine (default is entire image):
+%raw_size = size(GM.RawData);
+%GM.Params.XPixels = [0, raw_size(1) - 1];
+%GM.Params.YPixels = [0, raw_size(2) - 1];
+GM.Params.XPixels = [64, 127];
+GM.Params.YPixels = [64, 127];
+% Choose from which range of frames to display trajectories (default is all).
+%GM.Params.ZFrames = [1, raw_size(3)];
+GM.Params.ZFrames = [1, 100];
+GM.gui();

MATLAB/examples/Example_SPT_movie.m

@@ -40,6 +40,7 @@ G indicates a GPU is used.
 [Example_Publish_SMF](Example_Publish_SMF.m)                                    | as Example_Publish but using a pre-existing SMF
 [Example_SMLM_Basic](Example_SMLM_Basic.m)                                      | demonstrate basic SMLM functionality
 [Example_SMLM_script](Example_SMLM_script.m)                                    | example of SMLM analysis
+[Example_SPT_movie](Example_SPT_movie.m)                                        | produce a movie from SPT results
 [hierBaGoL_wrapper](hierBaGoL_wrapper.m)                                        | wrapper used to call BaGoL routines
 [generateBaGoLScripts](generateBaGoLScripts.m)                                  | generate a series of self-contained scripts to run BaGoL over a number of cells, one script per cell
 [BaGoL_TEMPLATE](BaGoL_TEMPLATE.m)                                              | BaGoL script template for generateBaGoLScripts

MATLAB/examples/README.md

@@ -24,6 +24,7 @@ SMITE code templates requiring user-supplied data:
    Example_Publish_SMF          as Example_Publish but using a pre-existing SMF
    Example_SMLM_Basic		demonstrate basic SMLM functionality
    Example_SMLM_script		example of SMLM analysis
+   Example_SPT_movie            produce a movie from SPT results
    hierBaGoL_wrapper		wrapper used to call BaGoL routines
    generateBaGoLScripts		generate a series of self-contained scripts to
 				run BaGoL over a number of cells, one script