napari-sprout 1.1.0__tar.gz

napari_sprout-1.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Yichen He
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

napari_sprout-1.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: napari-sprout
+Version: 1.1.0
+Summary: napari plugin for SPROUT: seeds, growing, editing and AI prompts for 2D and 3D segmentation
+Author: Yichen He
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/EchanHe/SPROUT
+Project-URL: Documentation, https://github.com/EchanHe/SPROUT#readme
+Project-URL: Issues, https://github.com/EchanHe/SPROUT/issues
+Project-URL: Changelog, https://github.com/EchanHe/SPROUT/blob/main/CHANGELOG.md
+Keywords: napari,segmentation,image analysis,micro-CT,CT,MRI,3D,multi-class
+Classifier: Framework :: napari
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: sprout-seg~=1.1.0
+Requires-Dist: napari>=0.6.1
+Requires-Dist: qtpy
+Requires-Dist: magicgui
+Requires-Dist: superqt
+Provides-Extra: all
+Requires-Dist: napari[all]; extra == "all"
+Provides-Extra: ai
+Requires-Dist: sprout-seg[ai]~=1.1.0; extra == "ai"
+Dynamic: license-file
+
+# napari-sprout
+
+The napari plugin of [SPROUT](https://github.com/EchanHe/SPROUT): multi-part segmentation of 2D and 3D greyscale images (e.g. CT, MRI) without training data.
+
+- **Seeds**: thresholds and erosion split an image into parts; adaptive and sweep modes combine several settings.
+- **Grow**: seeds grow back to the full shape of each part.
+- **Edit**: split, merge, relabel and clean regions.
+- **Prompt (AI)**: seeds as prompts for nnInteractive.
+- **ROI & Boundary**: work inside a region; make boundary masks.
+
+## Install
+
+```bash
+pip install "napari-sprout[all]"     # with napari and Qt
+pip install napari-sprout            # napari already installed
+```
+
+For the Prompt (AI) tab also run `pip install "sprout-seg[ai]"` (with an NVIDIA GPU, install PyTorch for your CUDA version first).
+
+## Use
+
+Start napari and open **Plugins → SPROUT**. Videos: [SPROUT playlist](https://www.youtube.com/watch?v=4DHI1gs1lzc&list=PL8tsvVKJ9n6FjYYplo-IAwKBLxDh578aj). Docs and the command line (`sprout`): [github.com/EchanHe/SPROUT](https://github.com/EchanHe/SPROUT).
+
+## Cite
+
+Y. He, M. Camaiti, L.E. Roberts, J.M. Mulqueeney, E. Ioannou, M. Didziokas, A. Goswami. *SPROUT: A User-friendly, Scalable Toolkit for Multi-class Segmentation of Volumetric Images.* [bioRxiv 2024](https://www.biorxiv.org/content/10.1101/2024.11.22.624847v2.abstract).
+
+MIT License.

napari_sprout-1.1.0/README.md

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+# napari-sprout
+
+The napari plugin of [SPROUT](https://github.com/EchanHe/SPROUT): multi-part segmentation of 2D and 3D greyscale images (e.g. CT, MRI) without training data.
+
+- **Seeds**: thresholds and erosion split an image into parts; adaptive and sweep modes combine several settings.
+- **Grow**: seeds grow back to the full shape of each part.
+- **Edit**: split, merge, relabel and clean regions.
+- **Prompt (AI)**: seeds as prompts for nnInteractive.
+- **ROI & Boundary**: work inside a region; make boundary masks.
+
+## Install
+
+```bash
+pip install "napari-sprout[all]"     # with napari and Qt
+pip install napari-sprout            # napari already installed
+```
+
+For the Prompt (AI) tab also run `pip install "sprout-seg[ai]"` (with an NVIDIA GPU, install PyTorch for your CUDA version first).
+
+## Use
+
+Start napari and open **Plugins → SPROUT**. Videos: [SPROUT playlist](https://www.youtube.com/watch?v=4DHI1gs1lzc&list=PL8tsvVKJ9n6FjYYplo-IAwKBLxDh578aj). Docs and the command line (`sprout`): [github.com/EchanHe/SPROUT](https://github.com/EchanHe/SPROUT).
+
+## Cite
+
+Y. He, M. Camaiti, L.E. Roberts, J.M. Mulqueeney, E. Ioannou, M. Didziokas, A. Goswami. *SPROUT: A User-friendly, Scalable Toolkit for Multi-class Segmentation of Volumetric Images.* [bioRxiv 2024](https://www.biorxiv.org/content/10.1101/2024.11.22.624847v2.abstract).
+
+MIT License.

napari_sprout-1.1.0/napari_sprout/__init__.py

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+"""napari-sprout: A napari plugin for SPROUT segmentation."""
+
+__version__ = "1.1.0"
+
+from ._widget import make_sprout_widget
+from ._widget import make_sprout_widget_edit
+from ._widget import make_sprout_widget_info
+from ._widget import make_sprout_widget_map
+
+__all__ = ["make_sprout_widget",
+              "make_sprout_widget_edit",
+              "make_sprout_widget_info",
+               "make_sprout_widget_map"
+           ]

napari_sprout-1.1.0/napari_sprout/_widget.py

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+"""Main widget for napari-SPROUT plugin."""
+
+from qtpy.QtWidgets import (
+    QWidget, QVBoxLayout, QTabWidget, QPushButton,
+    QLabel, QHBoxLayout, QFileDialog
+)
+# from qtpy.QtCore import Qt
+import napari
+from napari.utils.notifications import show_info, show_error
+import numpy as np
+import tifffile
+
+from .widgets.seed_widget import SeedGenerationWidget
+from .widgets.grow_widget import SeedGrowthWidget
+from .widgets.boundary_widget import BoundaryWidget
+from .widgets.prompt_tab import PromptTab
+from .utils.roi_widget import RoiTools
+
+from .widgets.info_widget import LayerInfoWidget
+from .widgets.edit_widget import QtLabelSelector
+from .widgets.map_widget import LabelMapperWidget
+from .widgets.tools_widget import SPROUTToolWidget
+
+class SPROUTWidget(QWidget):
+    """Main SPROUT widget containing all workflow steps."""
+    
+    def __init__(self, napari_viewer):
+        super().__init__()
+        self.viewer = napari_viewer
+        
+        self._init_ui()
+        self._connect_signals()
+    
+    def _init_ui(self):
+        """Initialize the user interface."""
+        layout = QVBoxLayout()
+        
+        # Set minimum size to ensure visibility
+        self.setMinimumSize(500, 500)
+        
+        # Header
+        header_layout = QHBoxLayout()
+        title = QLabel("<h4>SPROUT Segmentation</h2>")
+        header_layout.addWidget(title)
+        header_layout.addStretch()
+        
+        # Load image button
+        # self.load_btn = QPushButton("Load Image")
+        # header_layout.addWidget(self.load_btn)
+        
+        layout.addLayout(header_layout)
+        
+        # Info label
+        # info_text = (
+        #     "Semi-automated Parcellation of Region Outputs Using "
+        #     "Thresholding and Transformation"
+        # )
+        # info_label = QLabel(info_text)
+        # info_label.setWordWrap(True)
+        # info_label.setStyleSheet("QLabel { color: #666; }")
+        # layout.addWidget(info_label)
+        
+        # Tab widget for workflow steps
+        self.tabs = QTabWidget()
+        
+        # Create widgets for each step
+        self.seed_widget = SeedGenerationWidget(self.viewer)
+        self.grow_widget = SeedGrowthWidget(self.viewer)
+        self.prompt_tab = PromptTab(self.viewer)
+        self.boundary_widget = BoundaryWidget(self.viewer)
+
+        # ROI tools and the Boundary tab share the last tab (two sub-tabs)
+        self.roi_tools = RoiTools(self.viewer)
+        self.roi_boundary_tabs = QTabWidget()
+        self.roi_boundary_tabs.addTab(self.roi_tools, "ROI")
+        self.roi_boundary_tabs.addTab(self.boundary_widget, "Boundary")
+
+        # Add tabs
+        self.tabs.addTab(self.seed_widget, "1. Seeds")
+        self.tabs.addTab(self.grow_widget, "2. Grow")
+        self.tabs.addTab(self.prompt_tab, "3. Prompt (AI)")
+        self.tabs.addTab(self.roi_boundary_tabs, "ROI && Boundary")   # "&&": a single "&" is a Qt mnemonic
+        
+        layout.addWidget(self.tabs)
+        
+        
+        self.setLayout(layout)
+    
+    def _connect_signals(self):
+        """Connect widget signals."""
+        # self.load_btn.clicked.connect(self.load_image)
+        self.seed_widget.seeds_generated.connect(self._on_seeds_generated)
+        self.grow_widget.growth_completed.connect(self._on_growth_completed)
+        self.boundary_widget.boundary_created.connect(self._on_boundary_created)
+
+    def _on_boundary_created(self, name):
+        """Select a newly created boundary layer in the Seeds and Grow tabs."""
+        for w in (self.seed_widget, self.grow_widget):
+            w.boundary_combo.setCurrentText(name)
+
+    def load_image(self):
+        """Load an image file."""
+        filename, _ = QFileDialog.getOpenFileName(
+            self,
+            "Load Image",
+            "",
+            "Image Files (*.tif *.tiff);;All Files (*)"
+        )
+        
+        if filename:
+            try:
+                # Load image
+                image = tifffile.imread(filename)
+                
+                # Add to viewer
+                self.viewer.add_image(
+                    image,
+                    name=filename.split('/')[-1]
+                )
+                
+                # Refresh layer lists
+                self.seed_widget.refresh_layers()
+                self.grow_widget.refresh_layers()
+                
+                show_info(f"Loaded image: {filename}")
+                
+            except Exception as e:
+                show_error(f"Error loading image: {str(e)}")
+    
+    def _on_seeds_generated(self, seeds, sizes):
+        """Handle seed generation completion."""
+        # Switch to grow tab
+        self.tabs.setCurrentIndex(1)
+        
+        # Refresh grow widget layers
+        self.grow_widget.refresh_layers()
+        
+        show_info("Seeds generated! You can now edit them or proceed to growth.")
+    
+    def _on_growth_completed(self, result):
+        """Handle growth completion."""
+        show_info("Growth completed! You can save the result or continue editing.")
+
+
+def make_sprout_widget(viewer: "napari.viewer.Viewer" = None):
+    """Create the SPROUT widget.
+    
+    Parameters
+    ----------
+    viewer : napari.viewer.Viewer, optional
+        The napari viewer instance. If not provided, will get current viewer.
+        
+    Returns
+    -------
+    widget : SPROUTWidget
+        The SPROUT widget instance.
+    """
+    if viewer is None:
+        # Get the current viewer from napari
+        import napari
+        viewer = napari.current_viewer()
+        if viewer is None:
+            raise RuntimeError("No napari viewer found")
+    
+    widget = SPROUTWidget(viewer)
+    # no widget.show() in these factories: napari shows the widget when it docks it
+    # (a show() before that flashes it as a separate window)
+    return widget
+
+def make_sprout_widget_edit(viewer: "napari.viewer.Viewer" = None):
+    """Create the SPROUT widget for editing.
+    
+    Parameters
+    ----------
+    viewer : napari.viewer.Viewer, optional
+        The napari viewer instance. If not provided, will get current viewer.
+        
+    Returns
+    -------
+    widget : SPROUTWidget
+        The SPROUT widget instance.
+    """
+    if viewer is None:
+        # Get the current viewer from napari
+        import napari
+        viewer = napari.current_viewer()
+        if viewer is None:
+            raise RuntimeError("No napari viewer found")
+    
+    widget = QtLabelSelector(viewer)
+    return widget
+
+def make_sprout_widget_info(viewer: "napari.viewer.Viewer" = None):
+    """Create the SPROUT widget for information.
+    
+    Parameters
+    ----------
+    viewer : napari.viewer.Viewer, optional
+        The napari viewer instance. If not provided, will get current viewer.
+        
+    Returns
+    -------
+    widget : SPROUTWidget
+        The SPROUT widget instance.
+    """
+    if viewer is None:
+        # Get the current viewer from napari
+        import napari
+        viewer = napari.current_viewer()
+        if viewer is None:
+            raise RuntimeError("No napari viewer found")
+    
+    widget = LayerInfoWidget(viewer)
+    return widget
+
+
+def make_sprout_widget_map(viewer: "napari.viewer.Viewer" = None):
+    """Create the SPROUT widget for mapping.
+
+    Parameters
+    ----------
+    viewer : napari.viewer.Viewer, optional
+        The napari viewer instance. If not provided, will get current viewer.
+
+    Returns
+    -------
+    widget : SPROUTWidget
+        The SPROUT widget instance.
+    """
+    if viewer is None:
+        # Get the current viewer from napari
+        import napari
+        viewer = napari.current_viewer()
+        if viewer is None:
+            raise RuntimeError("No napari viewer found")
+
+    widget = LabelMapperWidget(viewer)
+    return widget
+
+
+def make_sprout_widget_tools(viewer: "napari.viewer.Viewer" = None):
+    """Create the SPROUT widget for tools.
+
+    Parameters
+    ----------
+    viewer : napari.viewer.Viewer, optional
+        The napari viewer instance. If not provided, will get current viewer.
+
+    Returns
+    -------
+    widget : SPROUTWidget
+        The SPROUT widget instance.
+    """
+    if viewer is None:
+        # Get the current viewer from napari
+        import napari
+        viewer = napari.current_viewer()
+        if viewer is None:
+            raise RuntimeError("No napari viewer found")
+
+    widget = SPROUTToolWidget(viewer)
+    return widget

napari_sprout-1.1.0/napari_sprout/layers/__init__.py

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+"""Layer handling for napari-sprout."""

napari_sprout-1.1.0/napari_sprout/napari.yaml

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+name: napari-sprout
+display_name: SPROUT
+contributions:
+  commands:
+    - id: napari-sprout.make_widget
+      python_name: napari_sprout._widget:make_sprout_widget
+      title: SPROUT Main Widget                  
+    
+    - id: napari-sprout.edit_widget
+      python_name: napari_sprout._widget:make_sprout_widget_edit
+      title: SPROUT Edit Labels                   
+    
+    - id: napari-sprout.info_widget
+      python_name: napari_sprout._widget:make_sprout_widget_info
+      title: SPROUT Data Info                     
+    
+    - id: napari-sprout.map_sprout
+      python_name: napari_sprout._widget:make_sprout_widget_map
+      title: SPROUT Label Mapping                 
+    - id: napari-sprout.tools_widget
+      python_name: napari_sprout._widget:make_sprout_widget_tools
+      title: SPROUT Batch Builder                  
+  widgets:
+    - command: napari-sprout.make_widget
+      display_name: SPROUT
+    - command: napari-sprout.edit_widget
+      display_name: Edit
+    - command: napari-sprout.map_sprout
+      display_name: Label Mapping
+    - command: napari-sprout.tools_widget
+      display_name: Batch Builder
+    - command: napari-sprout.info_widget
+      display_name: Data Info

napari_sprout-1.1.0/napari_sprout/utils/__init__.py

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+"""Utility functions for napari-sprout."""

napari_sprout-1.1.0/napari_sprout/utils/boundary_check.py

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+"""Check the boundary mask when Generate Seeds / Start Growth is clicked.
+
+A mask that cannot be used gives a red line under the Boundary combo (no dialog) and the
+run does not start.
+
+SPROUT needs a boundary with exactly two values (0 = keep, non-zero = boundary).
+Without this check a wrong layer only fails inside the background worker, with a
+less specific message.
+"""
+import numpy as np
+
+
+def boundary_problem(data):
+    """None if `data` works as a SPROUT boundary, else a short description.
+
+    Mirrors config_core.check_and_cast_boundary: bool, or exactly two values one of
+    which is 0. ~1 s on 1e9 voxels (np.unique would take ~20 s).
+    """
+    data = np.asarray(data)
+    if data.dtype == bool:
+        return None if data.any() else "it is empty (no boundary voxels)"
+    mx, mn = data.max(), data.min()
+    if mx == 0 and mn == 0:
+        return "it is empty (no boundary voxels)"
+    if mn != 0 and mx != 0 and not np.any(data == 0):
+        return "it has no 0 voxels (everything would be boundary)"
+    if np.any((data != 0) & (data != mx)):
+        step = max(1, int(round((data.size / 2e6) ** (1 / data.ndim))))
+        values = np.unique(data[(slice(None, None, step),) * data.ndim])
+        shown = ", ".join(str(v) for v in values[:6]) + (", ..." if values.size > 6 else "")
+        return f"it has more than two values ({shown})"
+    return None
+
+
+def boundary_message(name, problem):
+    return (f"The boundary mask '{name}' cannot be used: {problem}.\n"
+            "A boundary mask needs exactly two values: 0 = keep, non-zero = boundary.\n"
+            "Choose another layer, or set Boundary Mask to None.")
+
+
+def boundary_ok(parent, name, data, note=None):
+    """True if the boundary can be used; otherwise say why in `note` (the red line under
+    the Boundary combo, a utils.status.StatusLine) and return False. No dialog."""
+    if note is not None:
+        note.clear()
+    if data is None:
+        return True
+    problem = boundary_problem(data)
+    if problem is None:
+        return True
+    if note is not None:
+        note.set(boundary_message(name, problem), "error")
+    return False

napari_sprout-1.1.0/napari_sprout/utils/fit_table.py

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+"""A table as high as its rows (no empty filler), capped; it scrolls inside beyond that."""
+from qtpy.QtCore import QTimer
+from qtpy.QtWidgets import QSizePolicy, QTableWidget
+
+
+class FitTable(QTableWidget):
+    """Header + rows high, up to MAX_ROWS rows; an inner scrollbar beyond that.
+
+    The height follows row inserts / removals by itself (call fit() after anything else
+    that changes row heights). Full width: the columns stretch over it.
+    """
+
+    MAX_ROWS = 10
+
+    def __init__(self, *args, max_rows=None, auto_fit=True, **kwargs):
+        super().__init__(*args, **kwargs)
+        if max_rows is not None:
+            self.MAX_ROWS = max_rows
+        if auto_fit:
+            m = self.model()
+            for sig in (m.rowsInserted, m.rowsRemoved, m.modelReset, m.layoutChanged):
+                sig.connect(self._fit_later)
+            self.horizontalScrollBar().rangeChanged.connect(self._fit_if_alive)
+            self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
+            self.fit()
+
+    def _fit_later(self, *_):
+        self.fit()
+        QTimer.singleShot(0, self._fit_if_alive)      # row heights settle after the insert
+
+    def _fit_if_alive(self):
+        try:
+            self.fit()
+        except RuntimeError:                          # deleted meanwhile
+            pass
+
+    def fit(self):
+        n = min(self.rowCount(), self.MAX_ROWS)
+        h = 2 * self.frameWidth() + self.horizontalHeader().sizeHint().height()
+        h += sum(self.rowHeight(i) for i in range(n))
+        if self.horizontalScrollBar().maximum() > 0:     # columns wider than the table (not the header length:
+            # right after the vertical scrollbar appears it is briefly wider than the viewport)
+            h += self.horizontalScrollBar().sizeHint().height()
+        if self.minimumHeight() != h or self.maximumHeight() != h:
+            self.setFixedHeight(h)
+
+    def resizeEvent(self, event):
+        super().resizeEvent(event)
+        self.fit()                      # a narrower table may need its horizontal scrollbar