frontveg 0.2.0__tar.gz → 0.3.0__tar.gz

{frontveg-0.2.0 → frontveg-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: frontveg
-Version: 0.2.0
+Version: 0.3.0
 Summary: Segmentation of vegetation located to close to camera
 Author: Herearii Metuarea
 Author-email: herearii.metuarea@univ-angers.fr
@@ -50,13 +50,19 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Image Processing
-Requires-Python: >=3.10
+Requires-Python: ==3.11.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: magicgui
 Requires-Dist: qtpy
 Requires-Dist: scikit-image
+Requires-Dist: transformers==4.51.3
+Requires-Dist: torch>=2.3.1
+Requires-Dist: torchvision>=0.18.1
+Requires-Dist: hydra-core==1.3.2
+Requires-Dist: iopath>=0.1.10
+Requires-Dist: pillow>=9.4.0
 Provides-Extra: testing
 Requires-Dist: tox; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -83,8 +89,8 @@ A plugin for foreground vegetation segmentation, tailored for trellised vegetati
 
 The method was developped by Herearii Metuarea, PHENET PhD at LARIS (French laboratory located in Angers, France) and Abdoul-Djalil Hamza Ousseini, AgroEcoPhen Engineer at IRHS (French Institute located in INRAe Angers, France) in Imhorphen team (bioimaging research group lead) under the supervision of Eric Duchêne (Research Engineer), Morgane Roth (Research Engineer) and David Rousseau (Full professor). This plugin was written by Herearii Metuarea and was designed in the context of the european project PHENET.
 
+![Data Warehouse](https://github.com/user-attachments/assets/4a110408-5854-4e8c-b655-4cb588434b79)
 
-![Data Warehouse](https://github.com/user-attachments/assets/781dc1ef-3ae0-47ff-9771-6de2879ed602)
 
 ----------------------------------
 

{frontveg-0.2.0 → frontveg-0.3.0}/README.md

@@ -15,8 +15,8 @@ A plugin for foreground vegetation segmentation, tailored for trellised vegetati
 
 The method was developped by Herearii Metuarea, PHENET PhD at LARIS (French laboratory located in Angers, France) and Abdoul-Djalil Hamza Ousseini, AgroEcoPhen Engineer at IRHS (French Institute located in INRAe Angers, France) in Imhorphen team (bioimaging research group lead) under the supervision of Eric Duchêne (Research Engineer), Morgane Roth (Research Engineer) and David Rousseau (Full professor). This plugin was written by Herearii Metuarea and was designed in the context of the european project PHENET.
 
+![Data Warehouse](https://github.com/user-attachments/assets/4a110408-5854-4e8c-b655-4cb588434b79)
 
-![Data Warehouse](https://github.com/user-attachments/assets/781dc1ef-3ae0-47ff-9771-6de2879ed602)
 
 ----------------------------------
 

{frontveg-0.2.0 → frontveg-0.3.0}/pyproject.toml

@@ -23,12 +23,18 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Image Processing",
 ]
-requires-python = ">=3.10"
+requires-python = "==3.11.12"
 dependencies = [
     "numpy",
     "magicgui",
     "qtpy",
     "scikit-image",
+    "transformers==4.51.3",
+    "torch>=2.3.1",
+    "torchvision>=0.18.1",
+    "hydra-core==1.3.2",
+    "iopath>=0.1.10",
+    "pillow>=9.4.0",
 ]
 
 [project.optional-dependencies]

frontveg-0.3.0/src/frontveg/__init__.py

@@ -0,0 +1,9 @@
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+from ._widget import (
+    vegetation,
+)
+
+__all__ = ("vegetation",)

{frontveg-0.2.0 → frontveg-0.3.0}/src/frontveg/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.0'
-__version_tuple__ = version_tuple = (0, 2, 0)
+__version__ = version = '0.3.0'
+__version_tuple__ = version_tuple = (0, 3, 0)

frontveg-0.3.0/src/frontveg/_widget.py

@@ -0,0 +1,146 @@
+"""
+This module contains four napari widgets declared in
+different ways:
+
+- a pure Python function flagged with `autogenerate: true`
+    in the plugin manifest. Type annotations are used by
+    magicgui to generate widgets for each parameter. Best
+    suited for simple processing tasks - usually taking
+    in and/or returning a layer.
+- a `magic_factory` decorated function. The `magic_factory`
+    decorator allows us to customize aspects of the resulting
+    GUI, including the widgets associated with each parameter.
+    Best used when you have a very simple processing task,
+    but want some control over the autogenerated widgets. If you
+    find yourself needing to define lots of nested functions to achieve
+    your functionality, maybe look at the `Container` widget!
+- a `magicgui.widgets.Container` subclass. This provides lots
+    of flexibility and customization options while still supporting
+    `magicgui` widgets and convenience methods for creating widgets
+    from type annotations. If you want to customize your widgets and
+    connect callbacks, this is the best widget option for you.
+- a `QWidget` subclass. This provides maximal flexibility but requires
+    full specification of widget layouts, callbacks, events, etc.
+
+References:
+- Widget specification: https://napari.org/stable/plugins/building_a_plugin/guides.html#widgets
+- magicgui docs: https://pyapp-kit.github.io/magicgui/
+
+Replace code below according to your needs.
+"""
+
+from typing import TYPE_CHECKING
+
+import numpy as np
+import torch
+from magicgui import magic_factory
+from PIL import Image
+from scipy import ndimage
+from transformers import pipeline
+
+if TYPE_CHECKING:
+    import napari
+from frontveg.utils import frontground_part, ground_dino, sam2
+
+pipe = pipeline(
+    task="depth-estimation", model="depth-anything/Depth-Anything-V2-Large-hf"
+)
+
+
+@magic_factory(call_button="Run")
+def vegetation(
+    input_data: "napari.types.ImageData",
+) -> "napari.types.LabelsData":
+    device = "cuda"
+
+    if input_data.ndim == 4:
+        output_data = np.zeros(
+            (input_data.shape[0], input_data.shape[1], input_data.shape[2]),
+            dtype="uint8",
+        )
+        INPUT = []
+        for i in range(len(input_data)):
+            rgb_data = input_data[i, :, :, :].compute()
+            image = Image.fromarray(rgb_data)
+            INPUT.append(image)
+    else:
+        output_data = np.zeros(
+            (1, input_data.shape[0], input_data.shape[1]), dtype="uint8"
+        )
+        rgb_data = input_data
+        image = Image.fromarray(rgb_data)
+        INPUT = [image]
+    depth = pipe(INPUT)
+    n = len(depth)
+
+    model, processor = ground_dino()
+    predictor, text_labels = sam2()
+
+    for i in range(n):
+        depth_pred = depth[i]["depth"]
+        msks_depth = np.array(depth_pred)
+        msks_front = frontground_part(msks_depth)
+        msks_front = msks_front.astype(np.uint8) * 255
+
+        image = INPUT[i]
+        inputs = processor(
+            images=image, text=text_labels, return_tensors="pt"
+        ).to(device)
+        with torch.no_grad():
+            outputs = model(**inputs)
+
+        results = processor.post_process_grounded_object_detection(
+            outputs,
+            inputs.input_ids,
+            box_threshold=0.4,
+            text_threshold=0.3,
+            target_sizes=[image.size[::-1]],
+        )
+
+        # Retrieve the first image result
+        result = results[0]
+        for box, score, labels in zip(
+            result["boxes"], result["scores"], result["labels"], strict=False
+        ):
+            box = [round(x, 2) for x in box.tolist()]
+            print(
+                f"Detected {labels} with confidence {round(score.item(), 3)} at location {box}"
+            )
+        if len(result["boxes"]) == 0:
+            masks = np.zeros(image.size[::-1], dtype="uint8")
+        else:
+            with (
+                torch.inference_mode(),
+                torch.autocast("cuda", dtype=torch.bfloat16),
+            ):
+                predictor.set_image(image)
+                masks_sam, _, _ = predictor.predict(
+                    box=result["boxes"],
+                    point_labels=result["labels"],
+                    multimask_output=False,
+                )
+            if masks_sam.ndim == 4:
+                masks = np.sum(masks_sam, axis=0)
+                masks = masks[0, :, :]
+            else:
+                masks = masks_sam[0, :, :]
+
+        msks_veg = masks.astype(np.uint8) * 255
+
+        mask1 = msks_front.copy()  # Masque 1
+        mask2 = msks_veg.copy()  # Masque 2
+        mask2 = ndimage.binary_fill_holes(mask2)  # Fill holes
+        mask1 = (mask1 > 0).astype(np.uint8)  # Convertir en binaire
+        mask2 = (mask2 > 0).astype(np.uint8)  # Convertir en binaire
+        if len(np.unique(mask2)) == 2:
+            intersection = (
+                mask1 & mask2
+            )  # Intersection : les pixels qui sont 1 dans les deux masques
+            intersection = intersection > 0
+        else:
+            intersection = mask1.copy()
+        intersection = (intersection * 255).astype(
+            np.uint8
+        )  # Si tu veux un masque avec des 0 et 255 (ex. pour OpenCV)
+        output_data[i, :, :] = intersection
+    return output_data

frontveg-0.3.0/src/frontveg/napari.yaml

@@ -0,0 +1,14 @@
+name: frontveg
+display_name: Frontveg
+# use 'hidden' to remove plugin from napari hub search results
+visibility: public
+# see https://napari.org/stable/plugins/technical_references/manifest.html#fields for valid categories
+categories: ["Annotation", "Segmentation", "Acquisition"]
+contributions:
+  commands:
+    - id: frontveg.vegetation
+      python_name: frontveg:vegetation
+      title: Vegetation plugin
+  widgets:
+    - command: frontveg.vegetation
+      display_name: Frontground vegetation

frontveg-0.3.0/src/frontveg/utils.py

@@ -0,0 +1,109 @@
+import os
+from collections import Counter
+
+import matplotlib.pyplot as plt
+import numpy as np
+from scipy.signal import find_peaks
+from tqdm import tqdm
+from transformers import AutoModelForZeroShotObjectDetection, AutoProcessor
+
+# CONF = config.get_conf_dict()
+homedir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+
+# base_dir = CONF['general']['base_directory']
+base_dir = "."
+
+model_id = "IDEA-Research/grounding-dino-tiny"
+device = "cuda"
+
+processor = AutoProcessor.from_pretrained(model_id)
+model = AutoModelForZeroShotObjectDetection.from_pretrained(model_id).to(
+    device
+)
+
+
+def ground_dino():
+    return model, processor
+
+
+from sam2.sam2_image_predictor import SAM2ImagePredictor
+
+predictor = SAM2ImagePredictor.from_pretrained("facebook/sam2-hiera-large")
+text_labels = ["green region. foliage."]
+
+
+def sam2():
+    return predictor, text_labels
+
+
+def minimum_betw_max(dico_, visua=False):
+    Ax = list(dico_.keys())
+    Ay = list(dico_.values())
+
+    # Approximation par une régression polynomiale
+    x = Ax[1:]
+    y = Ay[1:]
+    degree = 14  # Choisissez le degré selon la complexité de la courbe
+    coefficients = np.polyfit(x, y, degree)
+    polynomial = np.poly1d(coefficients)
+
+    # Points lissés pour tracer la courbe
+    x_fit = np.linspace(min(x), max(x), 500)
+    y_fit = polynomial(x_fit)
+
+    # Détection des maxima
+    peaks, _ = find_peaks(y_fit)
+
+    peak_values = y_fit[peaks]
+    sorted_indices = np.argsort(peak_values)[
+        ::-1
+    ]  # Trier en ordre décroissant
+    top_two_peaks = peaks[
+        sorted_indices[:2]
+    ]  # Les indices des deux plus grands pics
+
+    # Trouver le minimum entre les deux maxima
+    x_min_range = x_fit[top_two_peaks[0] : top_two_peaks[1] + 1]
+    y_min_range = y_fit[top_two_peaks[0] : top_two_peaks[1] + 1]
+    minx = min([top_two_peaks[0], top_two_peaks[1]])
+    maxx = max([top_two_peaks[0], top_two_peaks[1]])
+    x_min_range = x_fit[minx : maxx + 1]
+    y_min_range = y_fit[minx : maxx + 1]
+    min_index = np.argmin(y_min_range)  # Index du minimum dans cette plage
+    x_min = x_min_range[min_index]
+    y_min = y_min_range[min_index]
+
+    if visua:
+        # Tracé
+        plt.scatter(x, y, color="blue")
+        plt.plot(x_fit, y_fit, color="red", label="Polynomial regression")
+        plt.scatter(
+            x_fit[top_two_peaks],
+            y_fit[top_two_peaks],
+            color="green",
+            label="Local maximum",
+        )
+        plt.scatter(x_min, y_min, color="orange", s=100, label="Local minimum")
+        plt.legend()
+        plt.xlabel("Depth pixel")
+        plt.ylabel("Count")
+        # plt.title('Approximation et détection des points maximum')
+        plt.show()
+    return x_min, y_min
+
+
+def frontground_part(depths):
+    depth_one = depths[:, :]
+    n, m = depth_one.shape
+    A = []
+    for i in tqdm(range(n)):
+        for j in range(m):
+            A.append([i, j, depth_one[i, j]])
+    X = np.array(A)
+
+    dico_ = Counter(X[:, 2])
+    min_coord = minimum_betw_max(dico_, visua=False)
+
+    th_ = min_coord[0]
+    msks_depth = depth_one > th_
+    return msks_depth

{frontveg-0.2.0 → frontveg-0.3.0}/src/frontveg.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: frontveg
-Version: 0.2.0
+Version: 0.3.0
 Summary: Segmentation of vegetation located to close to camera
 Author: Herearii Metuarea
 Author-email: herearii.metuarea@univ-angers.fr
@@ -50,13 +50,19 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Image Processing
-Requires-Python: >=3.10
+Requires-Python: ==3.11.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: magicgui
 Requires-Dist: qtpy
 Requires-Dist: scikit-image
+Requires-Dist: transformers==4.51.3
+Requires-Dist: torch>=2.3.1
+Requires-Dist: torchvision>=0.18.1
+Requires-Dist: hydra-core==1.3.2
+Requires-Dist: iopath>=0.1.10
+Requires-Dist: pillow>=9.4.0
 Provides-Extra: testing
 Requires-Dist: tox; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -83,8 +89,8 @@ A plugin for foreground vegetation segmentation, tailored for trellised vegetati
 
 The method was developped by Herearii Metuarea, PHENET PhD at LARIS (French laboratory located in Angers, France) and Abdoul-Djalil Hamza Ousseini, AgroEcoPhen Engineer at IRHS (French Institute located in INRAe Angers, France) in Imhorphen team (bioimaging research group lead) under the supervision of Eric Duchêne (Research Engineer), Morgane Roth (Research Engineer) and David Rousseau (Full professor). This plugin was written by Herearii Metuarea and was designed in the context of the european project PHENET.
 
+![Data Warehouse](https://github.com/user-attachments/assets/4a110408-5854-4e8c-b655-4cb588434b79)
 
-![Data Warehouse](https://github.com/user-attachments/assets/781dc1ef-3ae0-47ff-9771-6de2879ed602)
 
 ----------------------------------
 

{frontveg-0.2.0 → frontveg-0.3.0}/src/frontveg.egg-info/SOURCES.txt

@@ -13,6 +13,7 @@ src/frontveg/__init__.py
 src/frontveg/_version.py
 src/frontveg/_widget.py
 src/frontveg/napari.yaml
+src/frontveg/utils.py
 src/frontveg.egg-info/PKG-INFO
 src/frontveg.egg-info/SOURCES.txt
 src/frontveg.egg-info/dependency_links.txt

frontveg-0.3.0/src/frontveg.egg-info/requires.txt

@@ -0,0 +1,18 @@
+numpy
+magicgui
+qtpy
+scikit-image
+transformers==4.51.3
+torch>=2.3.1
+torchvision>=0.18.1
+hydra-core==1.3.2
+iopath>=0.1.10
+pillow>=9.4.0
+
+[testing]
+tox
+pytest
+pytest-cov
+pytest-qt
+napari
+pyqt5

frontveg-0.2.0/src/frontveg/__init__.py

@@ -1,17 +0,0 @@
-try:
-    from ._version import version as __version__
-except ImportError:
-    __version__ = "unknown"
-from ._widget import (
-    ExampleQWidget,
-    ImageThreshold,
-    threshold_autogenerate_widget,
-    threshold_magic_widget,
-)
-
-__all__ = (
-    "ExampleQWidget",
-    "ImageThreshold",
-    "threshold_autogenerate_widget",
-    "threshold_magic_widget",
-)

frontveg-0.2.0/src/frontveg/_widget.py

@@ -1,129 +0,0 @@
-"""
-This module contains four napari widgets declared in
-different ways:
-
-- a pure Python function flagged with `autogenerate: true`
-    in the plugin manifest. Type annotations are used by
-    magicgui to generate widgets for each parameter. Best
-    suited for simple processing tasks - usually taking
-    in and/or returning a layer.
-- a `magic_factory` decorated function. The `magic_factory`
-    decorator allows us to customize aspects of the resulting
-    GUI, including the widgets associated with each parameter.
-    Best used when you have a very simple processing task,
-    but want some control over the autogenerated widgets. If you
-    find yourself needing to define lots of nested functions to achieve
-    your functionality, maybe look at the `Container` widget!
-- a `magicgui.widgets.Container` subclass. This provides lots
-    of flexibility and customization options while still supporting
-    `magicgui` widgets and convenience methods for creating widgets
-    from type annotations. If you want to customize your widgets and
-    connect callbacks, this is the best widget option for you.
-- a `QWidget` subclass. This provides maximal flexibility but requires
-    full specification of widget layouts, callbacks, events, etc.
-
-References:
-- Widget specification: https://napari.org/stable/plugins/building_a_plugin/guides.html#widgets
-- magicgui docs: https://pyapp-kit.github.io/magicgui/
-
-Replace code below according to your needs.
-"""
-
-from typing import TYPE_CHECKING
-
-from magicgui import magic_factory
-from magicgui.widgets import CheckBox, Container, create_widget
-from qtpy.QtWidgets import QHBoxLayout, QPushButton, QWidget
-from skimage.util import img_as_float
-
-if TYPE_CHECKING:
-    import napari
-
-
-# Uses the `autogenerate: true` flag in the plugin manifest
-# to indicate it should be wrapped as a magicgui to autogenerate
-# a widget.
-def threshold_autogenerate_widget(
-    img: "napari.types.ImageData",
-    threshold: "float",
-) -> "napari.types.LabelsData":
-    return img_as_float(img) > threshold
-
-
-# the magic_factory decorator lets us customize aspects of our widget
-# we specify a widget type for the threshold parameter
-# and use auto_call=True so the function is called whenever
-# the value of a parameter changes
-@magic_factory(
-    threshold={"widget_type": "FloatSlider", "max": 1}, auto_call=True
-)
-def threshold_magic_widget(
-    img_layer: "napari.layers.Image", threshold: "float"
-) -> "napari.types.LabelsData":
-    return img_as_float(img_layer.data) > threshold
-
-
-# if we want even more control over our widget, we can use
-# magicgui `Container`
-class ImageThreshold(Container):
-    def __init__(self, viewer: "napari.viewer.Viewer"):
-        super().__init__()
-        self._viewer = viewer
-        # use create_widget to generate widgets from type annotations
-        self._image_layer_combo = create_widget(
-            label="Image", annotation="napari.layers.Image"
-        )
-        self._threshold_slider = create_widget(
-            label="Threshold", annotation=float, widget_type="FloatSlider"
-        )
-        self._threshold_slider.min = 0
-        self._threshold_slider.max = 1
-        # use magicgui widgets directly
-        self._invert_checkbox = CheckBox(text="Keep pixels below threshold")
-
-        # connect your own callbacks
-        self._threshold_slider.changed.connect(self._threshold_im)
-        self._invert_checkbox.changed.connect(self._threshold_im)
-
-        # append into/extend the container with your widgets
-        self.extend(
-            [
-                self._image_layer_combo,
-                self._threshold_slider,
-                self._invert_checkbox,
-            ]
-        )
-
-    def _threshold_im(self):
-        image_layer = self._image_layer_combo.value
-        if image_layer is None:
-            return
-
-        image = img_as_float(image_layer.data)
-        name = image_layer.name + "_thresholded"
-        threshold = self._threshold_slider.value
-        if self._invert_checkbox.value:
-            thresholded = image < threshold
-        else:
-            thresholded = image > threshold
-        if name in self._viewer.layers:
-            self._viewer.layers[name].data = thresholded
-        else:
-            self._viewer.add_labels(thresholded, name=name)
-
-
-class ExampleQWidget(QWidget):
-    # your QWidget.__init__ can optionally request the napari viewer instance
-    # use a type annotation of 'napari.viewer.Viewer' for any parameter
-    def __init__(self, viewer: "napari.viewer.Viewer"):
-        super().__init__()
-        self.viewer = viewer
-
-        btn = QPushButton("Click me!")
-        btn.clicked.connect(self._on_click)
-
-        self.setLayout(QHBoxLayout())
-        self.layout().addWidget(btn)
-
-    def _on_click(self):
-        print("napari has", len(self.viewer.layers), "layers")

frontveg-0.2.0/src/frontveg/napari.yaml

@@ -1,30 +0,0 @@
-name: frontveg
-display_name: Frontveg
-# use 'hidden' to remove plugin from napari hub search results
-visibility: public
-# see https://napari.org/stable/plugins/technical_references/manifest.html#fields for valid categories
-categories: ["Annotation", "Segmentation", "Acquisition"]
-contributions:
-  commands:
-    - id: frontveg.make_container_widget
-      python_name: frontveg:ImageThreshold
-      title: Make threshold Container widget
-    - id: frontveg.make_magic_widget
-      python_name: frontveg:threshold_magic_widget
-      title: Make threshold magic widget
-    - id: frontveg.make_function_widget
-      python_name: frontveg:threshold_autogenerate_widget
-      title: Make threshold function widget
-    - id: frontveg.make_qwidget
-      python_name: frontveg:ExampleQWidget
-      title: Make example QWidget
-  widgets:
-    - command: frontveg.make_container_widget
-      display_name: Container Threshold
-    - command: frontveg.make_magic_widget
-      display_name: Magic Threshold
-    - command: frontveg.make_function_widget
-      autogenerate: true
-      display_name: Autogenerate Threshold
-    - command: frontveg.make_qwidget
-      display_name: Example QWidget

frontveg-0.2.0/src/frontveg.egg-info/requires.txt

@@ -1,12 +0,0 @@
-numpy
-magicgui
-qtpy
-scikit-image
-
-[testing]
-tox
-pytest
-pytest-cov
-pytest-qt
-napari
-pyqt5