From 6d4916809888076950fd967f72571a0cceac8831 Mon Sep 17 00:00:00 2001
From: carlosuc3m <100329787@alumnos.uc3m.es>
Date: Tue, 29 Oct 2024 19:53:40 +0100
Subject: [PATCH] improve mask creation filling holes

---
 src/main/java/ai/nets/samj/models/EfficientSamJ.java    | 2 ++
 src/main/java/ai/nets/samj/models/EfficientViTSamJ.java | 2 ++
 src/main/java/ai/nets/samj/models/PythonMethods.java    | 3 +--
 src/main/java/ai/nets/samj/models/Sam2.java             | 2 ++
 4 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/main/java/ai/nets/samj/models/EfficientSamJ.java b/src/main/java/ai/nets/samj/models/EfficientSamJ.java
index 8669345..042a559 100644
--- a/src/main/java/ai/nets/samj/models/EfficientSamJ.java
+++ b/src/main/java/ai/nets/samj/models/EfficientSamJ.java
@@ -64,6 +64,7 @@ public class EfficientSamJ extends AbstractSamJ {
 			+ "from skimage import measure" + System.lineSeparator()
 			+ "measure.label(np.ones((10, 10)), connectivity=1)" + System.lineSeparator()
 			+ "import torch" + System.lineSeparator()
+			+ "from scipy.ndimage import binary_fill_holes" + System.lineSeparator()
 			+ "import sys" + System.lineSeparator()
 			+ "sys.path.append(r'%s')" + System.lineSeparator()
 			+ "from multiprocessing import shared_memory" + System.lineSeparator()
@@ -79,6 +80,7 @@ public class EfficientSamJ extends AbstractSamJ {
 			+ "globals()['measure'] = measure" + System.lineSeparator()
 			+ "globals()['np'] = np" + System.lineSeparator()
 			+ "globals()['torch'] = torch" + System.lineSeparator()
+			+ "globals()['binary_fill_holes'] = binary_fill_holes" + System.lineSeparator()
 			+ "globals()['predictor'] = predictor" + System.lineSeparator();
 
 	/**
diff --git a/src/main/java/ai/nets/samj/models/EfficientViTSamJ.java b/src/main/java/ai/nets/samj/models/EfficientViTSamJ.java
index 233b340..22e6939 100644
--- a/src/main/java/ai/nets/samj/models/EfficientViTSamJ.java
+++ b/src/main/java/ai/nets/samj/models/EfficientViTSamJ.java
@@ -79,6 +79,7 @@ public class EfficientViTSamJ extends AbstractSamJ {
 			+ "from skimage import measure" + System.lineSeparator()
 			+ "measure.label(np.ones((10, 10)), connectivity=1)" + System.lineSeparator()
 			+ "import torch" + System.lineSeparator()
+			+ "from scipy.ndimage import binary_fill_holes" + System.lineSeparator()
 			+ "import sys" + System.lineSeparator()
 			+ "import os" + System.lineSeparator()
 			+ "os.chdir(r'%s')" + System.lineSeparator()
@@ -107,6 +108,7 @@ public class EfficientViTSamJ extends AbstractSamJ {
 			+ "globals()['measure'] = measure" + System.lineSeparator()
 			+ "globals()['np'] = np" + System.lineSeparator()
 			+ "globals()['torch'] = torch" + System.lineSeparator()
+			+ "globals()['binary_fill_holes'] = binary_fill_holes" + System.lineSeparator()
 			+ "globals()['predictor'] = predictor" + System.lineSeparator();
 	/**
 	 * String containing the Python imports code after it has been formatted with the correct 
diff --git a/src/main/java/ai/nets/samj/models/PythonMethods.java b/src/main/java/ai/nets/samj/models/PythonMethods.java
index 7cb10d8..bb30c2b 100644
--- a/src/main/java/ai/nets/samj/models/PythonMethods.java
+++ b/src/main/java/ai/nets/samj/models/PythonMethods.java
@@ -89,8 +89,7 @@ public class PythonMethods {
 			+ "    for obj in labels:" + System.lineSeparator()
 			+ "        if obj.num_pixels >= at_least_of_this_size:" + System.lineSeparator()
 			+ "            x_coords,y_coords = trace_contour(obj.image, obj.num_pixels, obj.bbox[1],obj.bbox[0])" + System.lineSeparator()
-			+ "            rle = encode_rle(obj.image * 1)" + System.lineSeparator()
-			+ "            print(np.array(rle)[1::2])" + System.lineSeparator()
+			+ "            rle = encode_rle(binary_fill_holes(obj.image))" + System.lineSeparator()
 			+ "            bbox_w = obj.bbox[3] - obj.bbox[1]" + System.lineSeparator()
 			+ "            for i in range(0, len(rle), 2):" + System.lineSeparator()
 			+ "              rle[i] = sam_result.shape[1] * (obj.bbox[0] + rle[i] // bbox_w) + obj.bbox[1] + rle[i] % bbox_w" + System.lineSeparator()
diff --git a/src/main/java/ai/nets/samj/models/Sam2.java b/src/main/java/ai/nets/samj/models/Sam2.java
index 79938c6..adea456 100644
--- a/src/main/java/ai/nets/samj/models/Sam2.java
+++ b/src/main/java/ai/nets/samj/models/Sam2.java
@@ -75,6 +75,7 @@ public class Sam2 extends AbstractSamJ {
 			+ "from skimage import measure" + System.lineSeparator()
 			+ "measure.label(np.ones((10, 10)), connectivity=1)" + System.lineSeparator()
 			+ "import torch" + System.lineSeparator()
+			+ "from scipy.ndimage import binary_fill_holes" + System.lineSeparator()
 			+ "import sys" + System.lineSeparator()
 			+ "import os" + System.lineSeparator()
 			+ "from multiprocessing import shared_memory" + System.lineSeparator()
@@ -92,6 +93,7 @@ public class Sam2 extends AbstractSamJ {
 			+ "globals()['measure'] = measure" + System.lineSeparator()
 			+ "globals()['np'] = np" + System.lineSeparator()
 			+ "globals()['torch'] = torch" + System.lineSeparator()
+			+ "globals()['binary_fill_holes'] = binary_fill_holes" + System.lineSeparator()
 			+ "globals()['predictor'] = predictor" + System.lineSeparator();
 	/**
 	 * String containing the Python imports code after it has been formated with the correct