cellfinder 1.1.3__py3-none-any.whl → 1.3.0rc0__py3-none-any.whl

cellfinder/napari/utils.py

@@ -1,24 +1,10 @@
 from typing import List, Tuple
 
 import napari
+import napari.layers
 import numpy as np
-import pandas as pd
 from brainglobe_utils.cells.cells import Cell
-from pkg_resources import resource_filename
-
-brainglobe_logo = resource_filename(
-    "cellfinder", "napari/images/brainglobe.png"
-)
-
-
-widget_header = """
-<p>Efficient cell detection in large images.</p>
-<p><a href="https://brainglobe.info" style="color:gray;">Website</a></p>
-<p><a href="https://brainglobe.info/documentation/cellfinder/user-guide/napari-plugin/index.html" style="color:gray;">Documentation</a></p>
-<p><a href="https://github.com/brainglobe/cellfinder" style="color:gray;">Source</a></p>
-<p><a href="https://doi.org/10.1371/journal.pcbi.1009074" style="color:gray;">Citation</a></p>
-<p><small>For help, hover the cursor over each parameter.</small>
-"""  # noqa: E501
+from brainglobe_utils.qtpy.logo import header_widget
 
 
 def html_label_widget(label: str, *, tag: str = "b") -> dict:
@@ -31,25 +17,42 @@ def html_label_widget(label: str, *, tag: str = "b") -> dict:
     )
 
 
-header_label_widget = html_label_widget(
-    f"""
-<img src="{brainglobe_logo}"width="100">
-<p>cellfinder</p>
-""",
-    tag="h1",
-)
+def cellfinder_header():
+    """
+    Create the header containing the brainglobe logo and documentation links
+    for all cellfinder widgets.
+    """
+    return header_widget(
+        "cellfinder",
+        "Efficient cell detection in large images.",
+        documentation_path="cellfinder/user-guide/napari-plugin/index.html",
+        citation_doi="https://doi.org/10.1371/journal.pcbi.1009074",
+        help_text="For help, hover the cursor over each parameter.",
+    )
+
+
+# the xyz axis order in napari relative to ours. I.e. our zeroth axis is the
+# napari last axis. Ours is XYZ.
+napari_points_axis_order = 2, 1, 0
+# the xyz axis order in brainglobe relative to napari. I.e. napari's zeroth
+# axis is our last axis - it's just flipped
+brainglobe_points_axis_order = napari_points_axis_order
 
 
-def add_layers(points: List[Cell], viewer: napari.Viewer) -> None:
+def add_classified_layers(
+    points: List[Cell],
+    viewer: napari.Viewer,
+    unknown_name: str = "Rejected",
+    cell_name: str = "Detected",
+) -> None:
     """
-    Adds classified cell candidates as two separate point layers to the napari
-    viewer.
+    Adds cell candidates as two separate point layers - unknowns and cells, to
+    the napari viewer. Does not add any other cell types, only Cell.UNKNOWN
+    and Cell.CELL from the list of cells.
     """
-    detected, rejected = cells_to_array(points)
-
     viewer.add_points(
-        rejected,
-        name="Rejected",
+        cells_to_array(points, Cell.UNKNOWN, napari_order=True),
+        name=unknown_name,
         size=15,
         n_dimensional=True,
         opacity=0.6,
@@ -59,8 +62,8 @@ def add_layers(points: List[Cell], viewer: napari.Viewer) -> None:
         metadata=dict(point_type=Cell.UNKNOWN),
     )
     viewer.add_points(
-        detected,
-        name="Detected",
+        cells_to_array(points, Cell.CELL, napari_order=True),
+        name=cell_name,
         size=15,
         n_dimensional=True,
         opacity=0.6,
@@ -70,23 +73,61 @@ def add_layers(points: List[Cell], viewer: napari.Viewer) -> None:
     )
 
 
-def cells_df_as_np(
-    cells_df: pd.DataFrame,
-    new_order: List[int] = [2, 1, 0],
-    type_column: str = "type",
+def add_single_layer(
+    points: List[Cell],
+    viewer: napari.Viewer,
+    name: str,
+    cell_type: int,
+) -> None:
+    """
+    Adds all cells of cell_type Cell.TYPE to a new point layer in the napari
+    viewer, with given name.
+    """
+    viewer.add_points(
+        cells_to_array(points, cell_type, napari_order=True),
+        name=name,
+        size=15,
+        n_dimensional=True,
+        opacity=0.6,
+        symbol="ring",
+        face_color="lightskyblue",
+        visible=True,
+        metadata=dict(point_type=cell_type),
+    )
+
+
+def cells_to_array(
+    cells: List[Cell], cell_type: int, napari_order: bool = True
 ) -> np.ndarray:
     """
-    Convert a dataframe to an array, dropping *type_column* and re-ordering
-    the columns with *new_order*.
+    Converts all the cells of the given type as a 2D pos array.
+    The column order is either XYZ, otherwise it's the napari ordering
+    of the 3 axes (napari_points_axis_order).
     """
-    cells_df = cells_df.drop(columns=[type_column])
-    cells = cells_df[cells_df.columns[new_order]]
-    cells = cells.to_numpy()
-    return cells
+    cells = [c for c in cells if c.type == cell_type]
+    if not cells:
+        # make sure we return 2d array if cells is empty
+        return np.zeros((0, 3), dtype=np.int_)
+    points = np.array([(c.x, c.y, c.z) for c in cells])
 
+    if napari_order:
+        return points[:, napari_points_axis_order]
+    return points
 
-def cells_to_array(cells: List[Cell]) -> Tuple[np.ndarray, np.ndarray]:
-    df = pd.DataFrame([c.to_dict() for c in cells])
-    points = cells_df_as_np(df[df["type"] == Cell.CELL])
-    rejected = cells_df_as_np(df[df["type"] == Cell.UNKNOWN])
-    return points, rejected
+
+def napari_array_to_cells(
+    points: napari.layers.Points,
+    cell_type: int,
+    brainglobe_order: Tuple[int, int, int] = brainglobe_points_axis_order,
+) -> List[Cell]:
+    """
+    Takes a napari Points layer and returns a list of cell objects, one for
+    each point in the layer.
+    """
+    data = np.asarray(points.data)[:, brainglobe_order].tolist()
+
+    cells = []
+    for row in data:
+        cells.append(Cell(pos=row, cell_type=cell_type))
+
+    return cells

{cellfinder-1.1.3.dist-info → cellfinder-1.3.0rc0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.1.3
+Version: 1.3.0rc0
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -22,7 +22,7 @@ Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: brainglobe-utils >=0.4.2
+Requires-Dist: brainglobe-utils >=0.5.0
 Requires-Dist: brainglobe-napari-io >=0.3.4
 Requires-Dist: dask[array]
 Requires-Dist: fancylog >=0.0.7
@@ -31,10 +31,10 @@ Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
+Requires-Dist: keras >=3.0.0
+Requires-Dist: torch >=2.1.0
 Requires-Dist: tifffile
 Requires-Dist: tqdm
-Requires-Dist: tensorflow <2.12.0,>=2.5.0 ; platform_system != "Darwin" or platform_machine != "arm64"
-Requires-Dist: tensorflow-macos <2.12.0,>=2.5.0 ; platform_system == "Darwin" and platform_machine == "arm64"
 Provides-Extra: dev
 Requires-Dist: black ; extra == 'dev'
 Requires-Dist: pre-commit ; extra == 'dev'
@@ -54,17 +54,17 @@ Requires-Dist: napari[pyqt5] ; extra == 'napari'
 Requires-Dist: pooch >=1 ; extra == 'napari'
 Requires-Dist: qtpy ; extra == 'napari'
 
-[![Python Version](https://img.shields.io/pypi/pyversions/cellfinder-core.svg)](https://pypi.org/project/cellfinder)
-[![PyPI](https://img.shields.io/pypi/v/cellfinder-core.svg)](https://pypi.org/project/cellfinder)
-[![Downloads](https://pepy.tech/badge/cellfinder-core)](https://pepy.tech/project/cellfinder)
-[![Wheel](https://img.shields.io/pypi/wheel/cellfinder-core.svg)](https://pypi.org/project/cellfinder)
-[![Development Status](https://img.shields.io/pypi/status/cellfinder-core.svg)](https://github.com/brainglobe/cellfinder)
+[![Python Version](https://img.shields.io/pypi/pyversions/cellfinder.svg)](https://pypi.org/project/cellfinder)
+[![PyPI](https://img.shields.io/pypi/v/cellfinder.svg)](https://pypi.org/project/cellfinder)
+[![Downloads](https://pepy.tech/badge/cellfinder)](https://pepy.tech/project/cellfinder)
+[![Wheel](https://img.shields.io/pypi/wheel/cellfinder.svg)](https://pypi.org/project/cellfinder)
+[![Development Status](https://img.shields.io/pypi/status/cellfinder.svg)](https://github.com/brainglobe/cellfinder)
 [![Tests](https://img.shields.io/github/actions/workflow/status/brainglobe/cellfinder/test_and_deploy.yml?branch=main)](https://github.com/brainglobe/cellfinder/actions)
-[![codecov](https://codecov.io/gh/brainglobe/cellfinder-core/branch/main/graph/badge.svg?token=nx1lhNI7ox)](https://codecov.io/gh/brainglobe/cellfinder)
+[![codecov](https://codecov.io/gh/brainglobe/cellfinder/branch/main/graph/badge.svg?token=nx1lhNI7ox)](https://codecov.io/gh/brainglobe/cellfinder)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
-[![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://brainglobe.info/developers/index.html)
+[![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://brainglobe.info/community/developers/index.html)
 [![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
 
 # cellfinder

cellfinder-1.3.0rc0.dist-info/RECORD

@@ -0,0 +1,211 @@
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cellfinder/core/download/models.py

@@ -1,49 +0,0 @@
-import os
-from pathlib import Path
-from typing import Literal
-
-from cellfinder.core import logger
-from cellfinder.core.download.download import download
-
-model_weight_urls = {
-    "resnet50_tv": "https://gin.g-node.org/cellfinder/models/raw/"
-    "master/resnet50_tv.h5",
-    "resnet50_all": "https://gin.g-node.org/cellfinder/models/raw/"
-    "master/resnet50_weights.h5",
-}
-
-download_requirements_gb = {
-    "resnet50_tv": 0.18,
-    "resnet50_all": 0.18,
-}
-
-model_type = Literal["resnet50_tv", "resnet50_all"]
-
-
-def main(model_name: model_type, download_path: os.PathLike) -> Path:
-    """
-    For a given model name and download path, download the model file
-    and return the path to the downloaded file.
-    """
-    download_path = Path(download_path)
-
-    model_weight_dir = download_path / "model_weights"
-    model_path = model_weight_dir / f"{model_name}.h5"
-    if not model_path.exists():
-        model_weight_dir.mkdir(parents=True)
-
-        logger.info(
-            f"Downloading '{model_name}' model. This may take a little while."
-        )
-
-        download(
-            model_path,
-            model_weight_urls[model_name],
-            model_name,
-            download_requires=download_requirements_gb[model_name],
-        )
-
-    else:
-        logger.info(f"Model already exists at {model_path}. Skipping download")
-
-    return model_path

cellfinder/core/tools/IO.py

@@ -1,48 +0,0 @@
-import glob
-import os
-from typing import Tuple
-
-import numpy as np
-from brainglobe_utils.general.system import get_sorted_file_paths
-from dask import array as da
-from dask import delayed
-from tifffile import TiffFile, imread
-
-
-def get_tiff_meta(
-    path: str,
-) -> Tuple[Tuple[int, int], np.dtype]:
-    with TiffFile(path) as tfile:
-        nz = len(tfile.pages)
-        if not nz:
-            raise ValueError(f"tiff file {path} has no pages!")
-        first_page = tfile.pages[0]
-
-    return tfile.pages[0].shape, first_page.dtype
-
-
-lazy_imread = delayed(imread)  # lazy reader
-
-
-def read_with_dask(path):
-    """
-    Based on https://github.com/tlambert03/napari-ndtiffs
-    :param path:
-    :return:
-    """
-
-    if path.endswith(".txt"):
-        with open(path, "r") as f:
-            filenames = [line.rstrip() for line in f.readlines()]
-
-    else:
-        filenames = glob.glob(os.path.join(path, "*.tif"))
-
-    shape, dtype = get_tiff_meta(filenames[0])
-    lazy_arrays = [lazy_imread(fn) for fn in get_sorted_file_paths(filenames)]
-    dask_arrays = [
-        da.from_delayed(delayed_reader, shape=shape, dtype=dtype)
-        for delayed_reader in lazy_arrays
-    ]
-    stack = da.stack(dask_arrays, axis=0)
-    return stack

cellfinder/core/tools/tf.py

@@ -1,46 +0,0 @@
-import tensorflow as tf
-
-from cellfinder.core import logger
-
-
-def allow_gpu_memory_growth():
-    """
-    If a gpu is present, prevent tensorflow from using all the memory straight
-    away. Allows multiple processes to use the GPU (and avoid occasional
-    errors on some systems) at the cost of a slight performance penalty.
-    """
-    gpus = tf.config.experimental.list_physical_devices("GPU")
-    if gpus:
-        logger.debug("Allowing GPU memory growth")
-        try:
-            # Currently, memory growth needs to be the same across GPUs
-            for gpu in gpus:
-                tf.config.experimental.set_memory_growth(gpu, True)
-            logical_gpus = tf.config.experimental.list_logical_devices("GPU")
-            logger.debug(
-                f"{len(gpus)} physical GPUs, {len(logical_gpus)} logical GPUs"
-            )
-        except RuntimeError as e:
-            # Memory growth must be set before GPUs have been initialized
-            print(e)
-    else:
-        logger.debug("No GPUs found, using CPU.")
-
-
-def set_tf_threads(max_threads):
-    """
-    Limit the number of threads that tensorflow uses
-    :param max_threads: Maximum number of threads to use
-    :return:
-    """
-    logger.debug(
-        f"Setting maximum number of threads for tensorflow "
-        f"to: {max_threads}"
-    )
-
-    # If statements are for testing. If tf is initialised, then setting these
-    # parameters throws an error
-    if tf.config.threading.get_inter_op_parallelism_threads() != 0:
-        tf.config.threading.set_inter_op_parallelism_threads(max_threads)
-    if tf.config.threading.get_intra_op_parallelism_threads() != 0:
-        tf.config.threading.set_intra_op_parallelism_threads(max_threads)