Merge branch 'dev-MVC' of github.com:SystemsGenetics/granny into dev-MVC

Granny/Analyses/Segmentation.py

@@ -21,7 +21,7 @@
 from typing import Any, Dict, List, Tuple
 from urllib import request
 
-import matplotlib.pyplot as plt
+import cv2
 import numpy as np
 import pandas as pd
 from Granny.Analyses.Analysis import Analysis
@@ -33,7 +33,6 @@
 from Granny.Models.IO.RGBImageFile import RGBImageFile
 from Granny.Models.Values.FileNameValue import FileNameValue
 from Granny.Models.Values.ImageListValue import ImageListValue
-from matplotlib import patches
 from numpy.typing import NDArray
 
 
@@ -42,7 +41,7 @@ class SegmentationConfig:
     MODELS: Dict[str, Dict[str, str]] = {
         "pome_fruit-v1_0": {
             "full_name": "granny-v1_0-pome_fruit-v1_0.pt",
-            "url": "https://osf.io/dqzyn/download/",
+            "url": "https://osf.io/vyfhm/download/",
         }
     }
 
@@ -102,12 +101,12 @@ def __init__(self):
                 "tray_infos",
             )
         )
-        self.full_images = ImageListValue(
+        self.masked_images = ImageListValue(
             "f_img",
             "full_masked_image",
             "The output directory where the full-masked images are written.",
         )
-        self.full_images.setValue(
+        self.masked_images.setValue(
             os.path.join(
                 os.curdir,
                 "results",
@@ -126,7 +125,6 @@ def _getModelUrl(self, model_name: str):
         model_url = ""
         try:
             model_url = self.models[model_name]["url"]
-            print(f"Model URL: {model_url}")
         except KeyError:
             print(f"Key '{model_name}' not found in configuration.")
         return model_url
@@ -163,7 +161,7 @@ def _segmentInstances(self, image: NDArray[np.uint8]) -> List[Any]:
 
         return results
 
-    def _writeMaskedImage(self, tray_image: Image) -> None:
+    def _extractMaskedImage(self, tray_image: Image) -> Image:
         """"""
         [result] = tray_image.getSegmentationResults()
         masks = result.masks.cpu()
@@ -179,9 +177,9 @@ def _writeMaskedImage(self, tray_image: Image) -> None:
         hsv = [(i / num_instances, 1, brightness) for i in range(num_instances)]
         colors = list(map(lambda c: colorsys.hsv_to_rgb(*c), hsv))
         random.shuffle(colors)
-        _, ax = plt.subplots()
         for i in range(num_instances):
             mask = masks.data[i].numpy()
+            (r, g, b) = colors[i]
             for c in range(3):
                 result[:, :, c] = np.where(
                     mask == 1,
@@ -191,31 +189,21 @@ def _writeMaskedImage(self, tray_image: Image) -> None:
 
             x1, y1, x2, y2 = coords[i]
             x1, y1, x2, y2 = int(x1), int(y1), int(x2), int(y2)
-            ax.text(
-                x1, y1 + 10, "{:.3f}".format(confs[i]), color="w", size=7, backgroundcolor="none"
-            )
-            p = patches.Rectangle(
+            cv2.rectangle(result, (x1, y1), (x2, y2), (r * 255, g * 255, b * 255), 5)
+            cv2.putText(
+                result,
+                "{:.3f}".format(confs[i]),
                 (x1, y1),
-                x2 - x1,
-                y2 - y1,
-                linewidth=1,
-                edgecolor=colors[i],
-                facecolor="none",
-                linestyle="dashed",
+                fontFace=cv2.FONT_HERSHEY_SIMPLEX,
+                fontScale=2,
+                color=(255, 255, 255),
+                thickness=3,
             )
-            ax.add_patch(p)
-        plt.axis("off")
-        plt.imshow(result)
-        plt.tight_layout()
-        plt.savefig(
-            os.path.join(
-                self.full_images.getValue(),
-                tray_image.getImageName(),
-            ),
-            bbox_inches="tight",
-            pad_inches=0,
-            dpi=300,
+        image_instance: Image = RGBImage(
+            pathlib.Path(tray_image.getImageName()).stem + f"_masked_image" + ".png"
         )
+        image_instance.setImage(result)
+        return image_instance
 
     def _sortInstances(self, boxes: NDArray[np.float32], img_shape: Tuple[int, int]):
         """
@@ -370,6 +358,7 @@ def performAnalysis(self) -> List[Image]:
         # performs segmentation on each image one-by-one
         segmented_images: List[Image] = []
         tray_images: List[Image] = []
+        masked_images: List[Image] = []
         for image_instance in self.images:
             # set ImageIO with specific file path
             self.image_io.setFilePath(image_instance.getFilePath())
@@ -389,22 +378,30 @@ def performAnalysis(self) -> List[Image]:
             image_instance.setSegmentationResults(results=result)
 
             try:
-                # extracts individual instances and tray information
+                # extracts individual instances
                 image_instances = self._extractImage(image_instance)
-                tray_info = self._extractTrayInfo(image_instance)
+                # and tray information
+                tray_infos = self._extractTrayInfo(image_instance)
+                # and masked image
+                masked_image = self._extractMaskedImage(image_instance)
+
+                # save to list for output
                 segmented_images.extend(image_instances)
-                tray_images.extend(tray_info)
-                # writes masked image
-                self._writeMaskedImage(image_instance)
+                tray_images.extend(tray_infos)
+                masked_images.append(masked_image)
             except:
                 AttributeError("Error with the results.")
 
         # 1. sets the output ImageListValue with the list of segmented images
         # 2. writes the segmented images to "segmented_images" folder
         # 3. writes the tray information to "tray_info" folder
+        # 4. writes the full masked images to "full_masked_images" folder
         self.seg_images.setImageList(segmented_images)
         self.seg_images.writeValue()
 
         self.tray_infos.setImageList(tray_images)
         self.tray_infos.writeValue()
+
+        self.masked_images.setImageList(masked_images)
+        self.masked_images.writeValue()
         return segmented_images