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Added 4 new columns to the results table, ID, Min Dist to Surf, Max D… #1

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Added 4 new columns to the results table, ID, Min Dist to Surf, Max D… #1

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6 changes: 5 additions & 1 deletion src/main/java/Utilities/Counter3D.java
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Original file line number Diff line number Diff line change
Expand Up @@ -726,7 +726,7 @@ public void showStatistics(boolean newRT){
float calXYZ=(float) (cal.pixelWidth*cal.pixelHeight*cal.pixelDepth);
String unit=cal.getUnit();

String[] header={"Volume ("+unit+"^3)", "Surface ("+unit+"^2)", "Nb of obj. voxels", "Nb of surf. voxels", "IntDen", "Mean", "StdDev", "Median", "Min", "Max", "X", "Y", "Z", "Mean dist. to surf. ("+unit+")", "SD dist. to surf. ("+unit+")", "Median dist. to surf. ("+unit+")", "XM", "YM", "ZM", "BX", "BY", "BZ", "B-width", "B-height", "B-depth"};
String[] header={"ID", "Volume ("+unit+"^3)", "Surface ("+unit+"^2)", "Nb of obj. voxels", "Nb of surf. voxels", "IntDen", "Mean", "StdDev", "Median", "Min", "Max", "X", "Y", "Z", "Mean dist. to surf. ("+unit+")", "SD dist. to surf. ("+unit+")", "Median dist. to surf. ("+unit+")", "Min dist. to surf. ("+unit+")", "Max dist. to surf. ("+unit+")", "Max/Min dist. to surf. (Aspect ratio)", "XM", "YM", "ZM", "BX", "BY", "BZ", "B-width", "B-height", "B-depth"};
ResultsTable rt;

if (newRT){
Expand All @@ -741,6 +741,7 @@ public void showStatistics(boolean newRT){
rt.incrementCounter();
Object3D currObj=(Object3D) obj.get(i);

rt.setValue("ID", i, i+1);
if (Prefs.get("3D-OC-Options_volume.boolean", true)) rt.setValue("Volume ("+unit+"^3)", i, currObj.size*calXYZ);
if (Prefs.get("3D-OC-Options_surface.boolean", true)) rt.setValue("Surface ("+unit+"^2)", i, currObj.surf_cal);
if (Prefs.get("3D-OC-Options_objVox.boolean", true)) rt.setValue("Nb of obj. voxels", i, currObj.size);
Expand All @@ -763,6 +764,9 @@ public void showStatistics(boolean newRT){
if (Prefs.get("3D-OC-Options_meanDist2Surf.boolean", true)) rt.setValue("Mean dist. to surf. ("+unit+")", i, currObj.mean_dist2surf);
if (Prefs.get("3D-OC-Options_SDDist2Surf.boolean", true)) rt.setValue("SD dist. to surf. ("+unit+")", i, currObj.SD_dist2surf);
if (Prefs.get("3D-OC-Options_medDist2Surf.boolean", true)) rt.setValue("Median dist. to surf. ("+unit+")", i, currObj.median_dist2surf);
if (Prefs.get("3D-OC-Options_minDist2Surf.boolean", true)) rt.setValue("Min dist. to surf. ("+unit+")", i, currObj.min_dist2surf);
if (Prefs.get("3D-OC-Options_maxDist2Surf.boolean", true)) rt.setValue("Max dist. to surf. ("+unit+")", i, currObj.max_dist2surf);
if (Prefs.get("3D-OC-Options_aspectDist2Surf.boolean", true)) rt.setValue("Max/Min dist. to surf. (Aspect ratio)", i, currObj.aspect_dist2surf);

if (Prefs.get("3D-OC-Options_COM.boolean", true)){
float[] tmpArray=currObj.c_mass;
Expand Down
44 changes: 44 additions & 0 deletions src/main/java/Utilities/Object3D.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,15 @@ public class Object3D {

/**SD of the distance to the surface (distance calibrated measure)*/
public float SD_dist2surf;

/**Min distance to the surface (distance calibrated measure)*/
public float min_dist2surf;

/**Max distance to the surface (distance calibrated measure)*/
public float max_dist2surf;

/**Max/Min dist. to surf. (Aspect ratio)*/
public float aspect_dist2surf;

/**Object3D's size (in pixels or voxels)*/
public int size;
Expand Down Expand Up @@ -230,6 +239,9 @@ private void calcStats(){
if (surf_size!=1){
for (int i=0; i<surf_size; i++) SD_dist2surf+=Math.pow(dist2surfArray[i]-mean_dist2surf, 2);
median_dist2surf=median(dist2surfArray);
min_dist2surf=min(dist2surfArray);
max_dist2surf=max(dist2surfArray);
aspect_dist2surf=(float) max_dist2surf/min_dist2surf;
SD_dist2surf=(float) Math.sqrt(SD_dist2surf/(surf_size-1));
}

Expand Down Expand Up @@ -257,4 +269,36 @@ public float median(float[] array){

return med;
}

/**Calculates the min value of a float array.
* @param array input float array.
* @return the min value of the input float array (float).
*/
public float min(float[] array){
float min=0;
int index=0;

Arrays.sort(array);

min=array[0];

return min;
}

/**Calculates the max value of a float array.
* @param array input float array.
* @return the max value of the input float array (float).
*/
public float max(float[] array){
float max=0;
int index=0;

Arrays.sort(array);

max=array[array.length-1];

return max;
}


}
14 changes: 10 additions & 4 deletions src/main/java/_3D_OC_Options.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@
*/
public class _3D_OC_Options implements PlugIn{
public void run(String arg) {
String[] label=new String[16];
String[] label=new String[19];
boolean[] state=new boolean[label.length];

label[0]="Volume"; state[0]=Prefs.get("3D-OC-Options_volume.boolean", true);
Expand All @@ -51,8 +51,11 @@ public void run(String arg) {
label[11]="Mean_distance_to_surface"; state[11]=Prefs.get("3D-OC-Options_meanDist2Surf.boolean", true);
label[12]="Std_Dev_distance_to_surface"; state[12]=Prefs.get("3D-OC-Options_SDDist2Surf.boolean", true);
label[13]="Median_distance_to_surface"; state[13]=Prefs.get("3D-OC-Options_medDist2Surf.boolean", true);
label[14]="Centre_of_mass"; state[14]=Prefs.get("3D-OC-Options_COM.boolean", true);
label[15]="Bounding_box"; state[15]=Prefs.get("3D-OC-Options_BB.boolean", true);
label[14]="Min_distance_to_surface"; state[14]=Prefs.get("3D-OC-Options_minDist2Surf.boolean", true);
label[15]="Max_distance_to_surface"; state[15]=Prefs.get("3D-OC-Options_maxDist2Surf.boolean", true);
label[16]="Aspect-ratio_of_distance_to_surface"; state[16]=Prefs.get("3D-OC-Options_aspectDist2Surf.boolean", true);
label[17]="Centre_of_mass"; state[17]=Prefs.get("3D-OC-Options_COM.boolean", true);
label[18]="Bounding_box"; state[18]=Prefs.get("3D-OC-Options_BB.boolean", true);

boolean closeImg=Prefs.get("3D-OC-Options_closeImg.boolean", false);
boolean showMaskedImg=Prefs.get("3D-OC-Options_showMaskedImg.boolean", true);
Expand Down Expand Up @@ -81,7 +84,7 @@ public void run(String arg) {

GenericDialog gd=new GenericDialog("3D-OC Set Measurements");
gd.addMessage("Parameters to calculate:");
gd.addCheckboxGroup(8, 2, label, state);
gd.addCheckboxGroup(10, 2, label, state);
gd.addMessage("");
gd.addMessage("Image parameters:");
gd.addCheckbox("Close_original_images_while_processing_(saves_memory)", closeImg);
Expand Down Expand Up @@ -115,6 +118,9 @@ public void run(String arg) {
Prefs.set("3D-OC-Options_meanDist2Surf.boolean", gd.getNextBoolean());
Prefs.set("3D-OC-Options_SDDist2Surf.boolean", gd.getNextBoolean());
Prefs.set("3D-OC-Options_medDist2Surf.boolean", gd.getNextBoolean());
Prefs.set("3D-OC-Options_minDist2Surf.boolean", gd.getNextBoolean());
Prefs.set("3D-OC-Options_maxDist2Surf.boolean", gd.getNextBoolean());
Prefs.set("3D-OC-Options_aspectDist2Surf.boolean", gd.getNextBoolean());
Prefs.set("3D-OC-Options_COM.boolean", gd.getNextBoolean());
Prefs.set("3D-OC-Options_BB.boolean", gd.getNextBoolean());
Prefs.set("3D-OC-Options_closeImg.boolean", gd.getNextBoolean());
Expand Down