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ppouchinppouchin
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Merge pull request #12 from GReD-Clermont/refactoring
Small segmentation refactoring
2 parents bbfba3e + 57cfa06 commit c98a04b

14 files changed

Lines changed: 118 additions & 139 deletions

‎src/main/java/fr/igred/nucleus/dialogs/AutocropConfigDialog.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -60,7 +60,7 @@ public class AutocropConfigDialog extends JFrame implements ItemListener {
6060
private JPanel zCalibrationPanel;
6161

6262

63-
public AutocropConfigDialog(AutocropDialog caller) {
63+
public AutocropConfigDialog() {
6464
super.setTitle("Autocrop - NucleusJ3");
6565
super.setSize(600, 350);
6666
super.setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);

‎src/main/java/fr/igred/nucleus/dialogs/AutocropDialog.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -124,7 +124,7 @@ public AutocropDialog(IDialogListener dialogListener) {
124124
super.setMinimumSize(new Dimension(400, 500));
125125
super.setDefaultCloseOperation(DISPOSE_ON_CLOSE);
126126
super.setLocationRelativeTo(null);
127-
autocropConfigFileDialog = new AutocropConfigDialog(this);
127+
autocropConfigFileDialog = new AutocropConfigDialog();
128128
autocropConfigFileDialog.setVisible(false);
129129

130130
container = super.getContentPane();

‎src/main/java/fr/igred/nucleus/dialogs/SegmentationConfigDialog.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@
1717
*/
1818
package fr.igred.nucleus.dialogs;
1919

20-
import fr.igred.nucleus.core.NucleusSegmentation;
20+
import fr.igred.nucleus.utils.ConvexHullDetection;
2121

2222
import javax.swing.BorderFactory;
2323
import javax.swing.Box;
@@ -102,7 +102,7 @@ public SegmentationConfigDialog() {
102102
JPanel convexHullPane = new JPanel();
103103
convexHullPane.setLayout(new BoxLayout(convexHullPane, BoxLayout.LINE_AXIS));
104104
convexHullPane.setBorder(BorderFactory.createEmptyBorder(0, 10, 10, 10));
105-
JLabel zBox = new JLabel("Convex Hull Detection (" + NucleusSegmentation.CONVEX_HULL_ALGORITHM + ":");
105+
JLabel zBox = new JLabel("Convex Hull Detection (" + ConvexHullDetection.CONVEX_HULL_ALGORITHM + ":");
106106
convexHullPane.add(zBox);
107107
convexHullPane.add(Box.createRigidArea(new Dimension(10, 0)));
108108
convexHullDetection.setSelected(true);

src/main/java/fr/igred/nucleus/core/NucleusSegmentation.java renamed to src/main/java/fr/igred/nucleus/segmentation/NucleusSegmentation.java

Lines changed: 38 additions & 52 deletions
Original file line numberDiff line numberDiff line change
@@ -15,8 +15,12 @@
1515
* You should have received a copy of the GNU General Public License
1616
* along with this program. If not, see <http://www.gnu.org/licenses/>.
1717
*/
18-
package fr.igred.nucleus.core;
18+
package fr.igred.nucleus.segmentation;
1919

20+
import fr.igred.nucleus.core.Measure3D;
21+
import fr.igred.nucleus.utils.ConvexHullDetection;
22+
import fr.igred.nucleus.utils.ConvexHullSegmentation;
23+
import fr.igred.nucleus.utils.FillingHoles;
2024
import fr.igred.omero.Client;
2125
import fr.igred.omero.annotations.TagAnnotationWrapper;
2226
import fr.igred.omero.exception.AccessException;
@@ -28,8 +32,6 @@
2832
import fr.igred.omero.roi.RectangleWrapper;
2933
import fr.igred.nucleus.io.Directory;
3034
import fr.igred.nucleus.imageprocessing.Thresholding;
31-
import fr.igred.nucleus.segmentation.SegmentationParameters;
32-
import fr.igred.nucleus.utils.FillingHoles;
3335
import fr.igred.nucleus.utils.Gradient;
3436
import fr.igred.nucleus.utils.Histogram;
3537
import ij.ImagePlus;
@@ -69,33 +71,20 @@
6971
* @author Tristan Dubos and Axel Poulet
7072
*/
7173
public class NucleusSegmentation {
72-
/** Currently used algorithm to calculate nuclei convex hull */
73-
public static final String CONVEX_HULL_ALGORITHM = "GRAHAM";
7474

7575
/** Logger */
7676
private static final Logger LOGGER = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
7777

7878
/** Segmentation parameters for the analysis */
7979
private final SegmentationParameters segmentationParameters;
8080
/** ImagePlus input to process */
81-
private final ImagePlus imgRawTransformed;
82-
/** List of the 3D parameters computed associated to the segmented image */
83-
private Measure3D measure3D;
84-
/* String stocking the file name if any nucleus is detected*/
81+
private final ImagePlus imgRawTransformed;
8582
/** Threshold detected by the Otsu modified method */
8683
private int bestThreshold = -1;
87-
/** volume min of the detected object */
88-
private int vMin;
89-
/** volume max of the detected object */
90-
private int vMax;
9184
/** ImagePlus input to process */
9285
private ImagePlus imgRaw;
9386
/** Check if the segmentation is not in border */
9487
private boolean badCrop;
95-
/** Current image analysed */
96-
private File currentFile;
97-
/** String containing the output prefix */
98-
private String outputFilesPrefix;
9988
/** Segmented image */
10089
private ImagePlus[] imageSeg;
10190

@@ -104,36 +93,32 @@ public class NucleusSegmentation {
10493
* Constructor for the segmentation analysis for a folder containing images.
10594
*
10695
* @param imageFile Current image analysed
107-
* @param outputFilesPrefix prefix for the output file
108-
* @param segmentationParameters list the parameters for the analyse
96+
* @param params list the parameters for the analyse
10997
*
11098
* @throws IOException
11199
* @throws FormatException
112100
*/
113-
public NucleusSegmentation(File imageFile,
114-
String outputFilesPrefix,
115-
SegmentationParameters segmentationParameters)
101+
public NucleusSegmentation(File imageFile, SegmentationParameters params)
116102
throws IOException, FormatException {
117-
this.segmentationParameters = segmentationParameters;
118-
this.currentFile = imageFile;
119-
this.imgRaw = getImageChannel(0);
103+
this.segmentationParameters = params;
120104
// TODO ADD CHANNEL PARAMETERS (CASE OF CHANNELS UNSPLITED)
105+
this.imgRaw = getImageChannel(imageFile, 0);
121106
imgRaw.setTitle(imageFile.getName());
122107
this.imgRawTransformed = imgRaw.duplicate();
123108
imgRawTransformed.setTitle(imageFile.getName());
124-
Directory dirOutputOTSU = new Directory(segmentationParameters.getOutputFolder() + "OTSU");
109+
Directory dirOutputOTSU = new Directory(params.getOutputFolder() + "OTSU");
125110
dirOutputOTSU.checkAndCreateDir();
126-
if (segmentationParameters.getConvexHullDetection()) {
127-
Directory dirOutputConvexHull = new Directory(segmentationParameters.getOutputFolder() +
128-
CONVEX_HULL_ALGORITHM);
111+
if (params.getConvexHullDetection()) {
112+
Directory dirOutputConvexHull = new Directory(params.getOutputFolder() +
113+
ConvexHullDetection.CONVEX_HULL_ALGORITHM);
129114
dirOutputConvexHull.checkAndCreateDir();
130115
}
131116
}
132117

133118

134-
public NucleusSegmentation(ImageWrapper image, SegmentationParameters segmentationParameters, Client client)
119+
public NucleusSegmentation(ImageWrapper image, SegmentationParameters params, Client client)
135120
throws ServiceException, AccessException, ExecutionException {
136-
this.segmentationParameters = segmentationParameters;
121+
this.segmentationParameters = params;
137122

138123
int[] cBound = {0, 0};
139124
this.imgRaw = image.toImagePlus(client, null, null, cBound, null, null);
@@ -145,9 +130,8 @@ public NucleusSegmentation(ImageWrapper image, SegmentationParameters segmentati
145130

146131

147132
// Changed HERE TO RETRIEVE ONLY ID, ALLOWING MULTI THREADING DOWNLOAD
148-
public NucleusSegmentation(ImageWrapper image, ImagePlus imp, SegmentationParameters segmentationParameters,
149-
Client client) {
150-
this.segmentationParameters = segmentationParameters;
133+
public NucleusSegmentation(ImageWrapper image, ImagePlus imp, SegmentationParameters params) {
134+
this.segmentationParameters = params;
151135

152136
this.imgRaw = imp;
153137
// TODO ADD CHANNEL PARAMETERS (CASE OF CHANNELS UNSPLITED)
@@ -160,10 +144,10 @@ public NucleusSegmentation(ImageWrapper image, ImagePlus imp, SegmentationParame
160144
public NucleusSegmentation(ImageWrapper image,
161145
ROIWrapper roi,
162146
int i,
163-
SegmentationParameters segmentationParameters,
147+
SegmentationParameters params,
164148
Client client)
165149
throws ServiceException, AccessException, ExecutionException {
166-
this.segmentationParameters = segmentationParameters;
150+
this.segmentationParameters = params;
167151

168152
List<RectangleWrapper> rectangles = roi.getShapes().getElementsOf(RectangleWrapper.class);
169153

@@ -195,16 +179,17 @@ public NucleusSegmentation(ImageWrapper image,
195179
/**
196180
* Method to set a specific channel image
197181
*
198-
* @param channelNumber channel number of the current image to analyse
182+
* @param imageFile
183+
* @param channel channel number of the current image to analyse
199184
*
200185
* @return channel image
201186
*
202187
* @throws IOException
203188
* @throws FormatException
204189
*/
205-
public ImagePlus getImageChannel(int channelNumber) throws IOException, FormatException {
206-
ImagePlus[] currentImage = BF.openImagePlus(currentFile.getAbsolutePath());
207-
currentImage = ChannelSplitter.split(currentImage[channelNumber]);
190+
public static ImagePlus getImageChannel(File imageFile, int channel) throws IOException, FormatException {
191+
ImagePlus[] currentImage = BF.openImagePlus(imageFile.getAbsolutePath());
192+
currentImage = ChannelSplitter.split(currentImage[channel]);
208193
return currentImage[0];
209194
}
210195

@@ -217,7 +202,8 @@ public ImagePlus getImageChannel(int channelNumber) throws IOException, FormatEx
217202
* @return
218203
*/
219204
public String saveImageResult(ImagePlus[] segmentedImage) {
220-
this.measure3D = new Measure3D(segmentedImage, imgRaw, getXCalibration(), getYCalibration(), getZCalibration());
205+
Measure3D measure3D = new Measure3D(segmentedImage, imgRaw,
206+
getXCalibration(), getYCalibration(), getZCalibration());
221207
return measure3D.nucleusParameter3D();
222208
}
223209

@@ -294,7 +280,7 @@ public void findOTSUMaximisingSphericity() {
294280
}
295281

296282
if (bestThreshold != -1) {
297-
morphologicalCorrection(imageSeg[0]);
283+
imageSeg[0] = morphologicalCorrection(imageSeg[0]);
298284
checkBorder(imageSeg[0]);
299285
}
300286
}
@@ -424,7 +410,7 @@ public boolean isBadCrop() {
424410
* @return array lis which contain at the index 0 the min valu and index 1 the max value
425411
*/
426412
private static List<Integer> computeMinMaxThreshold(ImagePlus imagePlusInput) {
427-
List<Integer> arrayListMinMaxThreshold = new ArrayList<>();
413+
List<Integer> minMaxThreshold = new ArrayList<>(2);
428414

429415
int threshold = Thresholding.computeOTSUThreshold(imagePlusInput);
430416
StackStatistics stackStatistics = new StackStatistics(imagePlusInput);
@@ -433,12 +419,12 @@ private static List<Integer> computeMinMaxThreshold(ImagePlus imagePlusInput) {
433419
double max = threshold + stdDev / 2;
434420

435421
if (min < 0) {
436-
arrayListMinMaxThreshold.add(6);
422+
minMaxThreshold.add(6);
437423
} else {
438-
arrayListMinMaxThreshold.add((int) min);
424+
minMaxThreshold.add((int) min);
439425
}
440-
arrayListMinMaxThreshold.add((int) max);
441-
return arrayListMinMaxThreshold;
426+
minMaxThreshold.add((int) max);
427+
return minMaxThreshold;
442428
}
443429

444430

@@ -476,11 +462,11 @@ private static boolean isVoxelThresholded(ImagePlus imagePlusSegmented,
476462
*
477463
* @param imagePlusSegmented image to be correct
478464
*/
479-
private static void morphologicalCorrection(ImagePlus imagePlusSegmented) {
465+
private static ImagePlus morphologicalCorrection(ImagePlus imagePlusSegmented) {
480466
computeOpening(imagePlusSegmented);
481467
computeClosing(imagePlusSegmented);
482468
// TODO FIX?
483-
imagePlusSegmented = FillingHoles.apply2D(imagePlusSegmented);
469+
return FillingHoles.apply2D(imagePlusSegmented);
484470
}
485471

486472

@@ -780,9 +766,9 @@ public void saveOTSUSegmentedOMERO(Client client, Long output)
780766
public void saveConvexHullSeg() {
781767
LOGGER.info("Computing and saving Convex Hull segmentation.");
782768
if (!badCrop && bestThreshold != -1 && segmentationParameters.getConvexHullDetection()) {
783-
imageSeg[0] = ConvexHullSegmentation.convexHullDetection(imageSeg[0], segmentationParameters);
769+
imageSeg[0] = ConvexHullSegmentation.convexHullDetection(imageSeg[0]);
784770
String pathConvexHullSeg = segmentationParameters.getOutputFolder() +
785-
CONVEX_HULL_ALGORITHM + File.separator + imageSeg[0].getTitle();
771+
ConvexHullDetection.CONVEX_HULL_ALGORITHM + File.separator + imageSeg[0].getTitle();
786772
imageSeg[0].setTitle(pathConvexHullSeg);
787773
saveFile(imageSeg[0], pathConvexHullSeg);
788774
}
@@ -797,7 +783,7 @@ public void saveConvexHullSegOMERO(Client client, Long output)
797783
throws IOException, AccessException, ServiceException, ExecutionException, OMEROServerError {
798784
LOGGER.info("Computing and saving Convex Hull segmentation.");
799785
if (!badCrop && bestThreshold != -1 && segmentationParameters.getConvexHullDetection()) {
800-
imageSeg[0] = ConvexHullSegmentation.convexHullDetection(imageSeg[0], segmentationParameters);
786+
imageSeg[0] = ConvexHullSegmentation.convexHullDetection(imageSeg[0]);
801787

802788
String path = new java.io.File(".").getCanonicalPath() //+ File.separator + CONVEX_HULL_ALGORITHM
803789
+ File.separator + imageSeg[0].getTitle();

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