napari-piscis 0.1.20__py3-none-any.whl

napari_piscis/__init__.py

@@ -0,0 +1 @@
+from ._version import __version__

napari_piscis/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.1.20'
+__version_tuple__ = version_tuple = (0, 1, 20)
+
+__commit_id__ = commit_id = None

napari_piscis/_widget.py

@@ -0,0 +1,261 @@
+from __future__ import annotations
+
+import warnings
+from typing import TYPE_CHECKING, Tuple, List, Union, Dict, Any, Optional
+
+import numpy as np
+import napari
+from napari.qt.threading import thread_worker
+from napari.utils.notifications import show_info, show_warning, show_error
+from magicgui import magic_factory
+from loguru import logger
+
+try:
+    from skimage.color import rgb2gray
+    from piscis import Piscis
+    from piscis.utils import pad_and_stack
+    DEPENDENCIES_INSTALLED = True
+except ImportError as e:
+    DEPENDENCIES_INSTALLED = False
+    Piscis = None
+    pad_and_stack = None
+    rgb2gray = None
+
+if TYPE_CHECKING:
+    import napari.layers
+    import napari.types
+
+
+# --- 1. Pure Scientific Logic ---
+
+def infer_img_axes(shape: tuple) -> str:
+    """Infers axes (e.g. 'yx', 'zyx') from shape."""
+    if len(shape) == 2:
+        return 'yx'
+    elif len(shape) == 3:
+        if shape[-1] in (3, 4):
+            return 'yxc'
+        min_dim_idx = shape.index(min(shape))
+        low_dim_shape = list(shape)
+        low_dim_shape.pop(min_dim_idx)
+        low_dim_axes = infer_img_axes(tuple(low_dim_shape))
+        return low_dim_axes[:min_dim_idx] + 'z' + low_dim_axes[min_dim_idx:]
+    else:
+        raise ValueError(f"Image shape {shape} is not supported.")
+
+def run_inference_logic(
+    raw_image: np.ndarray,
+    model_name: str,
+    threshold: float,
+    min_distance: int,
+    intermediates: bool
+) -> Dict[str, Any]:
+    """Pure python function to run PISCIS inference."""
+    if not DEPENDENCIES_INSTALLED:
+        raise ImportError("PISCIS or skimage not installed.")
+
+    # 1. Analyze Input
+    axes = infer_img_axes(raw_image.shape)
+    logger.info(f"Input Shape {raw_image.shape}, Inferred axes {axes}")
+
+    is_3d_stack = 'z' in axes
+    
+    # 2. Initialize Model
+    model = Piscis(model_name=model_name)
+    
+    # 3. Preprocess
+    images_batch = None
+    processed_image_for_display = None 
+    was_color_converted = False
+
+    if is_3d_stack:
+        if axes == 'zyx':
+            images_batch = raw_image
+        elif axes == 'yxz':
+            images_batch = np.moveaxis(raw_image, -1, 0)
+        else:
+            raise ValueError(f"Unsupported 3D axis pattern: {axes}")
+    else:
+        if axes == 'yx':
+            images_batch = np.expand_dims(raw_image, axis=0)
+        elif axes == 'yxc':
+            gray_img = rgb2gray(raw_image)
+            images_batch = gray_img 
+            processed_image_for_display = gray_img
+            was_color_converted = True
+        else:
+            raise ValueError(f"Unsupported 2D axis pattern: {axes}")
+
+    # 4. Pad and Stack
+    images_padded = pad_and_stack(images_batch)
+
+    # 5. Predict
+    logger.info("PISCIS: Predicting...")
+    coords_pred, features = model.predict(
+        images_padded, 
+        threshold=threshold, 
+        intermediates=intermediates, 
+        min_distance=min_distance,
+        stack=is_3d_stack
+    )
+    
+    return {
+        'coords': coords_pred,
+        'features': features,
+        'is_3d_stack': is_3d_stack,
+        'padded_shape': images_padded.shape,
+        'processed_image': processed_image_for_display,
+        'was_color_converted': was_color_converted
+    }
+
+
+# --- 2. Worker Thread ---
+
+@thread_worker
+def piscis_worker(
+    raw_image: np.ndarray,
+    model_name: str,
+    threshold: float,
+    min_distance: int,
+    intermediates: bool
+):
+    try:
+        return run_inference_logic(
+            raw_image, model_name, threshold, min_distance, intermediates
+        )
+    except Exception as e:
+        raise e
+
+
+# --- 3. Visualization Helper ---
+
+def _display_features(viewer: napari.Viewer, features: Any, is_3d_stack: bool, layer_name: str):
+    """Parses PISCIS feature maps and adds them to the Napari viewer."""
+    features_np = np.array(features)
+    
+    try:
+        if is_3d_stack:
+            # Handle 3D Stacks
+            if features_np.ndim == 5:
+                feats = features_np[0] 
+            elif features_np.ndim == 4:
+                feats = features_np
+            else:
+                raise ValueError(f"Unexpected 3D shape: {features_np.shape}")
+            
+            if feats.shape[0] >= 2:
+                disp_y = features_np[:, 0, :, :]
+                disp_x = features_np[:, 1, :, :]
+                
+                viewer.add_image(disp_y, name=f"Disp Y ({layer_name})", visible=False)
+                viewer.add_image(disp_x, name=f"Disp X ({layer_name})", visible=False)
+
+            if feats.shape[0] > 2:
+                labels = features_np[:, 2, :, :]
+                viewer.add_image(labels, name=f"Labels ({layer_name})", visible=False)
+                pooled = features_np[:, 3, :, :]
+                viewer.add_image(pooled, name=f"Pooled Labels ({layer_name})", visible=False)
+
+        else:
+            # Handle 2D Images
+            if features_np.ndim == 4:
+                feats = features_np[0]
+            else:
+                feats = features_np
+            
+            if feats.shape[0] >= 2:
+                
+                viewer.add_image(feats[0], name=f"Disp Y ({layer_name})", visible=False)
+                viewer.add_image(feats[1], name=f"Disp X ({layer_name})", visible=False)
+
+            if feats.shape[0] > 2:
+                viewer.add_image(feats[2], name=f"Labels ({layer_name})", visible=False)
+                viewer.add_image(feats[3], name=f"Pooled Labels ({layer_name})", visible=False)
+                
+    except Exception as e:
+        logger.error(f"Error parsing features: {e}")
+        show_error(f"Error displaying features: {e}")
+        viewer.add_image(features_np, name=f"Raw Features ({layer_name})")
+
+
+# --- 4. Main Widget ---
+
+@magic_factory(
+    call_button="Run PISCIS",
+    layout="vertical",
+    image_layer={"label": "Select Input"},
+    model_name={"label": "Model Name", "choices": ["20230905"]},
+    threshold={"label": "Threshold", "min": 0.0, "max": 1.0, "step": 0.1, "value": 1.0, "tooltip": "Minimum pixels for a spot."},
+    min_distance={"label": "Min Distance", "min": 0, "max": 20, "step": 1, "value": 1},
+    intermediates={"label": "Return Feature Maps", "value": False},
+)
+def piscis_inference(
+    viewer: napari.Viewer,
+    image_layer: "napari.layers.Image",
+    model_name: str = "20230905",
+    threshold: float = 1.0,
+    min_distance: int = 1,
+    intermediates: bool = False,
+):
+    if not DEPENDENCIES_INSTALLED:
+        show_error("PISCIS dependencies not found. Please install: pip install piscis scikit-image")
+        return
+    if image_layer is None:
+        show_warning("Please select an image layer.")
+        return
+
+    raw_image = np.asarray(image_layer.data)
+    show_info(f"PISCIS: Preparing input...")
+
+    worker = piscis_worker(
+        raw_image,
+        model_name,
+        threshold,
+        int(min_distance),
+        intermediates
+    )
+
+    def on_success(result):
+        coords_pred = result['coords']
+        features = result['features']
+        is_3d_stack = result['is_3d_stack']
+        was_color_converted = result['was_color_converted']
+        processed_image = result['processed_image']
+        
+        # 1. Handle Color Conversion
+        if was_color_converted and processed_image is not None:
+            show_warning(f"Color input detected. Converted to grayscale for processing.")
+            
+            viewer.add_image(
+                processed_image, 
+                name=f"Grayscale Input ({image_layer.name})",
+                colormap='gray'
+            )
+            # Hide the original RGB layer
+            image_layer.visible = False
+        
+        # 2. Handle Coordinates
+        if len(coords_pred) > 0:
+            viewer.add_points(
+                np.array(coords_pred),
+                name=f"Spots ({image_layer.name})",
+                size=3,
+                face_color='lime',
+                symbol='disc',
+            )
+            show_info(f"PISCIS: Detected {len(coords_pred)} spots.")
+        else:
+            show_info("PISCIS: No spots detected.")
+
+        # 3. Handle Feature Maps
+        if intermediates and features is not None:
+             _display_features(viewer, features, is_3d_stack, image_layer.name)
+
+    def on_error(e):
+        show_error(f"PISCIS failed: {str(e)}")
+        # Loguru syntax to attach the exception object 'e' for a traceback
+        logger.opt(exception=e).error("Worker failed")
+
+    worker.returned.connect(on_success)
+    worker.errored.connect(on_error)
+    worker.start()

napari_piscis/napari.yaml

@@ -0,0 +1,10 @@
+name: napari-piscis
+display_name: Piscis
+contributions:
+  commands:
+    - id: napari-piscis.inference
+      title: "Piscis: Inference"
+      python_name: napari_piscis._widget:piscis_inference
+  widgets:
+    - command: napari-piscis.inference
+      display_name: "Piscis Inference"

napari_piscis-0.1.20.dist-info/METADATA

@@ -0,0 +1,98 @@
+Metadata-Version: 2.4
+Name: napari-piscis
+Version: 0.1.20
+Summary: Napari plugin for Piscis spot detection (smFISH)
+Author-email: Michael Blodgett <michaelablodgett@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2023-2024 William Niu
+        
+        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.
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: <3.14,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: napari>=0.4.19
+Requires-Dist: magicgui>=0.8
+Requires-Dist: numpy
+Requires-Dist: scikit-image
+Requires-Dist: piscis>=0.2.7
+Requires-Dist: jax<=0.4.30
+Requires-Dist: loguru
+Provides-Extra: all
+Requires-Dist: napari[all]; extra == "all"
+Dynamic: license-file
+
+# napari-piscis
+
+[![License MIT](https://img.shields.io/pypi/l/napari-piscis.svg?color=green)](https://github.com/p5ithurism/napari-piscis/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-piscis.svg?color=green)](https://pypi.org/project/napari-piscis)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-piscis.svg?color=green)](https://python.org)
+[![tests](https://github.com/p5ithurism/napari-piscis/workflows/tests/badge.svg)](https://github.com/p5ithurism/napari-piscis/actions)
+[![codecov](https://codecov.io/gh/p5ithurism/napari-piscis/branch/main/graph/badge.svg)](https://codecov.io/gh/p5ithurism/napari-piscis)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-piscis)](https://napari-hub.org/plugins/napari-piscis)
+[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+
+Unofficial napari plugin for [Piscis](https://github.com/zjniu/Piscis), a deep learning algorithm for spot detection.
+
+----------------------------------
+
+This [napari] plugin was based off of the [napari-plugin-template].
+
+## Installation
+
+You can install `napari-piscis` via [pip]:
+
+```
+pip install napari-piscis
+```
+
+## License
+
+Distributed under the terms of the [MIT] license,
+"napari-piscis" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue] along with a detailed description.
+
+[napari]: https://github.com/napari/napari
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+[napari-plugin-template]: https://github.com/napari/napari-plugin-template
+
+[napari]: https://github.com/napari/napari
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

napari_piscis-0.1.20.dist-info/RECORD

@@ -0,0 +1,10 @@
+napari_piscis/__init__.py,sha256=WjDmvecyDIyJLYp4rCV9vsSYbQDc4L1EpYqORvEXliI,33
+napari_piscis/_version.py,sha256=P88Jfo9OvOr8LB0vHFqLUwFR7A0eE281KxEewbcCSBc,706
+napari_piscis/_widget.py,sha256=T-V5eskIFJghOHGW526QTedMyAle0xjaOM3g_DktG9Q,8447
+napari_piscis/napari.yaml,sha256=6X-K-Y_dbNdn9TGjA1YzGKCpBbdA9_dmB9HdEABE5lQ,281
+napari_piscis-0.1.20.dist-info/licenses/LICENSE,sha256=83k71GgrPZSt4JsOf6KiAyi3_XL3kdmiexDLLYWvCTI,1072
+napari_piscis-0.1.20.dist-info/METADATA,sha256=8_iuvEH3QD5PVoIJYFOe6m4mXDIYl2lPcDJxzCKRWUg,4476
+napari_piscis-0.1.20.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+napari_piscis-0.1.20.dist-info/entry_points.txt,sha256=rXFKdNsiSm17cVGs3vJzP6SnKPllUkk3EaWrQNQlMQo,60
+napari_piscis-0.1.20.dist-info/top_level.txt,sha256=vKkzMwrBPY9PlqL5WNKJB-V1lNXwTioDpIh_p2bSjEk,14
+napari_piscis-0.1.20.dist-info/RECORD,,

napari_piscis-0.1.20.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

napari_piscis-0.1.20.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[napari.manifest]
+napari-piscis = napari_piscis:napari.yaml

napari_piscis-0.1.20.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023-2024 William Niu
+
+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_piscis-0.1.20.dist-info/top_level.txt

@@ -0,0 +1 @@
+napari_piscis