fucciphase 0.0.2__py3-none-any.whl → 0.0.4__py3-none-any.whl

fucciphase/utils/trackmate.py

@@ -1,7 +1,7 @@
 import re
 import xml.etree.ElementTree as et
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Any
 
 import numpy as np
 import pandas as pd
@@ -46,7 +46,7 @@ class TrackMateXML:
         List of all features in the xml file, and whether they are integer features.
     """
 
-    def __init__(self, xml_path: Union[str, Path]) -> None:
+    def __init__(self, xml_path: str | Path) -> None:
         """Initialize the TrackMateXML object.
 
         The xml file is parsed and the model and all spots are imported.
@@ -55,18 +55,35 @@ class TrackMateXML:
         ----------
         xml_path : Union[str, Path]
             Path to the xml file.
+
+        Raises
+        ------
+        FileNotFoundError
+            If the XML file does not exist.
+        ValueError
+            If the XML file is malformed or not a valid TrackMate file.
         """
         # parse tree
-        self._tree: et.ElementTree[et.Element[str]] = et.parse(xml_path)
+        xml_path = Path(xml_path)
+        if not xml_path.exists():
+            raise FileNotFoundError(f"TrackMate XML file not found: {xml_path}")
+
+        try:
+            self._tree: et.ElementTree[et.Element[str]] = et.parse(xml_path)
+        except et.ParseError as e:
+            raise ValueError(
+                f"Failed to parse TrackMate XML file {xml_path}: {e}"
+            ) from None
+
         self._root: et.Element | Any = self._tree.getroot()
 
         # placeholders
-        self._model: Optional[et.Element] = None
-        self._allspots: Optional[et.Element] = None
+        self._model: et.Element | None = None
+        self._allspots: et.Element | None = None
 
         self.nspots: int = 0  # number of spots
-        self.features: Dict[str, type] = {}  # features and their types
-        self.spot_features: List[str] = []  # list of spot features
+        self.features: dict[str, type] = {}  # features and their types
+        self.spot_features: list[str] = []  # list of spot features
 
         # import model and all spots
         self._import_data()
@@ -74,7 +91,7 @@ class TrackMateXML:
     def _get_spot_features(self) -> None:
         """Get the spot features from the tree."""
         if self._allspots is not None:
-            spot_features: List[str] = []
+            spot_features: list[str] = []
             for frame in self._allspots:
                 for spot in frame:
                     spot_features.extend(spot.attrib.keys())
@@ -249,7 +266,7 @@ class TrackMateXML:
                         for feature in new_features:
                             spot.attrib[feature] = str(spot_df[feature].values[0])
 
-    def save_xml(self, xml_path: Union[str, Path]) -> None:
+    def save_xml(self, xml_path: str | Path) -> None:
         """Save the xml file.
 
         Parameters
@@ -262,12 +279,12 @@ class TrackMateXML:
 
     def get_full_tracks(
         df: pd.DataFrame,
-        channels: List[str],
+        channels: list[str],
         track_id_name: str = "UNIQUE_TRACK_ID",
         spot_name: str = "name",
         frame_name: str = "FRAME",
         min_length: int = 40,
-    ) -> Tuple[List[pd.DataFrame], List[pd.DataFrame]]:
+    ) -> tuple[list[pd.DataFrame], list[pd.DataFrame]]:
         """Locate all tracks that may describe a full cycle.
         Tracks need to be auto-named by TrackMate.
         For example, Track_1a, Track_1aa, Track_1b etc.
@@ -275,8 +292,8 @@ class TrackMateXML:
         In addition, tracks longer than a certain minimum length can be selected.
         """
         regex = "Track_[0-9]+.[a-z]+"
-        candidate_tracks: List[pd.DataFrame] = []
-        save_tracks: List[pd.DataFrame] = []
+        candidate_tracks: list[pd.DataFrame] = []
+        save_tracks: list[pd.DataFrame] = []
         track_ids = df[track_id_name].unique()
         for track_id in track_ids:
             track = df[df[track_id_name] == track_id]

fucciphase-0.0.4.dist-info/METADATA

@@ -0,0 +1,238 @@
+Metadata-Version: 2.4
+Name: fucciphase
+Version: 0.0.4
+Summary: Cell cycle analysis plugin.
+Project-URL: homepage, https://github.com/nobias-ht/fucciphase
+Project-URL: repository, https://github.com/nobias-ht/fucciphase
+Author-email: Joran Deschamps <joran.deschamps@fht.org>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.10
+Requires-Dist: dtaidistance
+Requires-Dist: lineagetree<1.5.0
+Requires-Dist: matplotlib
+Requires-Dist: monotonic-derivative
+Requires-Dist: numpy
+Requires-Dist: openpyxl
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: svgwrite
+Provides-Extra: dev
+Requires-Dist: ipython; extra == 'dev'
+Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: pdbpp; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: rich; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == 'doc'
+Provides-Extra: jupyter
+Requires-Dist: jupyter; extra == 'jupyter'
+Provides-Extra: napari
+Requires-Dist: bioio; extra == 'napari'
+Requires-Dist: bioio-ome-tiff; extra == 'napari'
+Requires-Dist: bioio-tifffile; extra == 'napari'
+Requires-Dist: napari; extra == 'napari'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Description-Content-Type: text/markdown
+
+# fucciphase
+
+[![License](https://img.shields.io/pypi/l/fucciphase.svg?color=green)](https://github.com/Synthetic-Physiology-Lab/fucciphase/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/fucciphase.svg?color=green)](https://pypi.org/project/fucciphase)
+[![Python Version](https://img.shields.io/pypi/pyversions/fucciphase.svg?color=green)](https://python.org)
+[![CI](https://github.com/Synthetic-Physiology-Lab/fucciphase/actions/workflows/ci.yml/badge.svg)](https://github.com/Synthetic-Physiology-Lab/fucciphase/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/Synthetic-Physiology-Lab/fucciphase/branch/main/graph/badge.svg)](https://codecov.io/gh/Synthetic-Physiology-Lab/fucciphase)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/Synthetic-Physiology-Lab/fucciphase/main.svg)](https://results.pre-commit.ci/latest/github/Synthetic-Physiology-Lab/fucciphase/main)
+
+FUCCI cell cycle analysis plugin. Obtain cell cycle information from FUCCI fluorescence intensities.
+
+## Installation
+The best way to run fucciphase is to install it in a virtual conda environment.
+Make sure that git is installed and can be called from the command line.
+
+To install from pip:
+
+```bash
+pip install fucciphase
+```
+
+If you wish to install it from source:
+    
+```bash
+git clone https://github.com/Synthetic-Physiology-Lab/fucciphase
+cd fucciphase
+pip install -e .
+```
+
+The installation should not take longer than a few seconds (depending on your internet connection).
+
+A minimal environment for running the [notebooks](examples/notebooks) can be set up with:
+
+```bash
+pip install fucciphase jupyter matplotlib pandas
+````
+
+### Install Napari + movie reading support (optional)
+
+FUCCIphase does not install Napari by default. For .ome.tif visualisation, install:
+```bash
+pip install napari bioio bioio-ome-tiff bioio-tifffile
+```
+or, if installing from source with extras:
+```bash
+pip install -e ".[napari]"
+```
+---
+## What’s Inside This Repository
+
+This repository is organized to support both **analysis workflows** and **reproducible usage examples** of FUCCIphase.
+If you're new to the tool, this is where to start.
+
+### 1 — `examples/notebooks/` [📁 notebooks](examples/notebooks)
+
+Interactive Jupyter workflows demonstrating how to use FUCCIphase in practical scenarios.
+
+| Notebook                           | Purpose                                                        |
+| ---------------------------------- |----------------------------------------------------------------|
+| `extract_calibration_data.ipynb`   | Convert raw movies + TrackMate XML into FUCCI reference curves |
+| `sensor_calibration.ipynb`         | Build a FUCCI sensor model from calibration traces             |
+| `getting_started.ipynb`            | Minimal end-to-end example of FUCCIphase usage                 |
+| `example_estimated.ipynb`          | Visualize fucciphase output tables                             |
+| `percentage_reconstruction.ipynb`  | Smooth and reconstruct %phase trajectories                     |
+| `example_reconstruction.ipynb`     | Recover incomplete/noisy fluorescence traces                   |
+| `example_simulated.ipynb`          | Generate synthetic FUCCI signals for testing                   |
+| `color-tails-by-percentage.ipynb`  | Visualize population-level phase composition                   |
+| `explanation-dtw-alignment.ipynb`  | How DTW alignment works internally                             |
+| `phaselocking-workflow-lazy.ipynb` | Scalable phase-locking for large datasets                      |
+---
+
+### 2 — `examples/reproducibility/` [📁 reproducibility](examples/reproducibility)
+
+This is a minimal workflow that uses the sample data. Navigate to the reproducibility directory, then run the following command in one step:
+
+```bash
+fucciphase inputs/merged_linked.ome.xml `
+          -ref ../example_data/hacat_fucciphase_reference.csv `
+          -dt 0.25 `
+          -m MEAN_INTENSITY_CH1 `
+          -c MEAN_INTENSITY_CH2 `
+          --generate_unique_tracks true `
+```
+and to visualize results in napari:
+
+```bash
+fucciphase-napari outputs/merged_linked.ome_processed.csv inputs/downscaled_hacat.ome.tif -m 0 -c 1 -s 2 --pixel_size 0.544
+```
+
+Below a preview of the output generated by the reproducibility workflow:
+
+[![Preview of the video](examples/reproducibility/outputs/thumbnail.png)](outputs/video_downscaled_hacat.mp4)
+
+---
+
+### 3 — `examples/example_data/` [📁 example_data](examples/example_data)
+
+Reference-style FUCCI datasets used for **calibration & sensor building**.
+
+Includes:
+
+| File               | Meaning                                           |
+| ------------------ | ------------------------------------------------- |
+| `*_reference.csv`  | FUCCI calibration traces used to learn the sensor |
+| `*.json`           | Saved sensor models usable via CLI or notebooks   |
+
+Use this folder if you want to train your own sensor or understand expected input format.
+
+---
+## Basic usage
+
+Fucci phase currently supports loading a 
+[TrackMate](https://imagej.net/plugins/trackmate/) XML file:
+
+```python
+from fucciphase import process_trackmate
+from fucciphase.sensor import get_fuccisa_default_sensor
+
+trackmate_xml = "path/to/trackmate.xml"
+channel1 = "MEAN_INTENSITY_CH3"
+channel2 = "MEAN_INTENSITY_CH4"
+
+sensor = get_fuccisa_default_sensor()
+
+df = process_trackmate(trackmate_xml,
+                       channels=[channel1, channel2],
+		       sensor=sensor,
+                       thresholds=[0.1, 0.1])
+print(df)
+```
+The TrackMate XML is converted to a [Pandas](https://pandas.pydata.org/) DataFrame.
+Thus, in general data (e.g., stored in a CSV or XLSX file) that can be parsed into
+a DataFrame is supported.
+
+The runtime of the scripts depends on your datasize. 2D samples with a few hundred to a few thousand cells
+can be processed in a few minutes. Visualization in Napari can take a bit longer.
+Standard processing does not require a powerful computer.
+Make sure that you have sufficient RAM to load videos for visualization in Napari.
+
+### Using your own data
+
+To process your own dataset:
+
+1. Export tracking from Fiji/TrackMate as `.xml`
+
+
+2. Build a reference CSV (minimum one full cell cycle):
+
+   ```
+   percentage, time, cyan, magenta
+   ```
+   For reference, check the example files available in the `example_data` folder.
+
+
+3. Run:
+
+   ```bash
+   fucciphase your_tracks.xml -ref your_reference.csv -dt <your timestep> -m <ch1> -c <ch2>
+   ```
+4. Visualize with:
+
+   ```bash
+   fucciphase-napari your_tracks_processed.csv your_video.ome.tif -m <ch1> -c <ch2> -s <mask>
+   ```
+
+---
+## Development
+
+To develop fucciphase, clone the repository, install fucciphase in your environment
+and install the pre-commit hooks:
+
+```bash
+git clone https://github.com/Synthetic-Physiology-Lab/fucciphase
+cd fucciphase
+pip install -e ".[test, dev]"
+pre-commit install
+```
+
+If you want to build the documentation, replace the abovementioned pip install by:
+```bash
+pip install -e ".[test, dev, doc]"
+```
+---
+
+## Cite us
+
+Di Sante, M., Pezzotti, M., Zimmermann, J., Enrico, A., Deschamps, J., Balmas, E.,
+Becca, S., Solito, S., Reali, A., Bertero, A., Jug, F. and Pasqualini, F.S., 2025.
+CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies.
+bioRxiv, https://doi.org/10.1101/2024.12.19.629259

fucciphase-0.0.4.dist-info/RECORD

@@ -0,0 +1,25 @@
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+fucciphase/__main__.py,sha256=lXUDkaeNRAZep5O7dNLj9RY4EclpPolruAll0FFC_jo,298
+fucciphase/fucci_phase.py,sha256=34EmEaG_jEGvRMBocPRYfBYXSJpko3_nYUgP013Bkjo,8990
+fucciphase/io.py,sha256=5a8Qre5KCT1haoqsB8FELyPKM7hzPM9kcEBGclokSPA,2018
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+fucciphase/phase.py,sha256=wxBJoglCtnLTpZwJ2j1kUeKZMb3y3pqeKakjMSIn1bw,25450
+fucciphase/plot.py,sha256=0bLCJBdfR-I7_qNDurY4iJyeV8D0GqBTvHZO4NSNTlk,24212
+fucciphase/py.typed,sha256=esB4cHc6c07uVkGtqf8at7ttEnprwRxwk8obY8Qumq4,187
+fucciphase/sensor.py,sha256=XVshjhe6ix8FO5xmICLF7ovBCf_JcEkD328tU40-dj0,15172
+fucciphase/tracking_utilities.py,sha256=dJ0q903_aF7bJyARU7wPeRjX6r7b-sHWJVOyXucpMcI,4825
+fucciphase/napari/__init__.py,sha256=At9Shk6HfDf6obtQaM0yKG4NOZVO6YxD2-J1M2ZGm7w,198
+fucciphase/napari/tracks_to_napari.py,sha256=ITqm_aw1uRG-RIfuxoC-zJLCDmrxjduWbiWC69xGzMM,4060
+fucciphase/utils/__init__.py,sha256=YwgK2COtG44QJaXHVPYKu2-Ifm6GIG1ahykvJ4pr-MM,1408
+fucciphase/utils/checks.py,sha256=o4mMGJMIE5wlaf0jtblnTD4JGTfjc5W7ZS4tYDIPlLo,625
+fucciphase/utils/dtw.py,sha256=6RJ5wZ8jDFKSVmcYajsdTJ4tfe3E-wKROEA2rWyGRN4,1638
+fucciphase/utils/normalize.py,sha256=EyVDeMJrDu02XfSwt0jIUecAlTN9v9BAS2KdU5wKk_c,7173
+fucciphase/utils/phase_fit.py,sha256=tiZ7rVkPvFokf7ghhGfkcdr1udjptUU4HmKu53EL3LQ,1835
+fucciphase/utils/simulator.py,sha256=fV-Pj6APms3QbYmiD9TjEYYkTqkIWk0uKDLCpz36HmA,2323
+fucciphase/utils/track_postprocessing.py,sha256=AOm4N4WACzKymX7vz74HWeAIQx556OQ5IS6uHZHgvHw,14500
+fucciphase/utils/trackmate.py,sha256=NeP8vCQEAGiKwz2O0kDmmvJtkxHN6LBtDwkAHsZJrvg,11131
+fucciphase-0.0.4.dist-info/METADATA,sha256=JNqZF53wGiKLnWceUHEYXj1sim9p8TgftwNoRrnWHrk,9019
+fucciphase-0.0.4.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+fucciphase-0.0.4.dist-info/entry_points.txt,sha256=B77Cm5QnxeQz6DEfqD6n7zDw48-HrlepWPwLbdVITMY,119
+fucciphase-0.0.4.dist-info/licenses/LICENSE,sha256=pQGrOGpOTwikEzkZ8Zc9XLQwbaZ85TMJP-GaWCNZciw,1554
+fucciphase-0.0.4.dist-info/RECORD,,

{fucciphase-0.0.2.dist-info → fucciphase-0.0.4.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any

fucciphase-0.0.2.dist-info/METADATA

@@ -1,137 +0,0 @@
-Metadata-Version: 2.4
-Name: fucciphase
-Version: 0.0.2
-Summary: Cell cycle analysis plugin.
-Project-URL: homepage, https://github.com/nobias-ht/fucciphase
-Project-URL: repository, https://github.com/nobias-ht/fucciphase
-Author-email: Joran Deschamps <joran.deschamps@fht.org>
-License: BSD-3-Clause
-License-File: LICENSE
-Classifier: Development Status :: 3 - Alpha
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
-Requires-Dist: dtaidistance
-Requires-Dist: lineagetree<1.5.0
-Requires-Dist: matplotlib
-Requires-Dist: monotonic-derivative
-Requires-Dist: numpy
-Requires-Dist: openpyxl
-Requires-Dist: pandas
-Requires-Dist: scipy
-Requires-Dist: svgwrite
-Provides-Extra: dev
-Requires-Dist: ipython; extra == 'dev'
-Requires-Dist: mypy; extra == 'dev'
-Requires-Dist: pdbpp; extra == 'dev'
-Requires-Dist: pre-commit; extra == 'dev'
-Requires-Dist: rich; extra == 'dev'
-Requires-Dist: ruff; extra == 'dev'
-Provides-Extra: doc
-Requires-Dist: sphinx; extra == 'doc'
-Provides-Extra: jupyter
-Requires-Dist: jupyter; extra == 'jupyter'
-Provides-Extra: test
-Requires-Dist: pytest; extra == 'test'
-Requires-Dist: pytest-cov; extra == 'test'
-Description-Content-Type: text/markdown
-
-# fucciphase
-
-[![License](https://img.shields.io/pypi/l/fucciphase.svg?color=green)](https://github.com/Synthetic-Physiology-Lab/fucciphase/raw/main/LICENSE)
-[![PyPI](https://img.shields.io/pypi/v/fucciphase.svg?color=green)](https://pypi.org/project/fucciphase)
-[![Python Version](https://img.shields.io/pypi/pyversions/fucciphase.svg?color=green)](https://python.org)
-[![CI](https://github.com/Synthetic-Physiology-Lab/fucciphase/actions/workflows/ci.yml/badge.svg)](https://github.com/Synthetic-Physiology-Lab/fucciphase/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/Synthetic-Physiology-Lab/fucciphase/branch/main/graph/badge.svg)](https://codecov.io/gh/Synthetic-Physiology-Lab/fucciphase)
-[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/Synthetic-Physiology-Lab/fucciphase/main.svg)](https://results.pre-commit.ci/latest/github/Synthetic-Physiology-Lab/fucciphase/main)
-
-FUCCI cell cycle analysis plugin.
-Obtain cell cycle information from FUCCI fluorescence intensities.
-
-## Installation
-
-The best way to run fucciphase is to install it in a virtual conda environment.
-Make sure that git is installed and can be called from the command line.
-
-To install from pip:
-
-```bash
-pip install fucciphase
-```
-
-If you wish to install it from source:
-    
-```bash
-git clone https://github.com/Synthetic-Physiology-Lab/fucciphase
-cd fucciphase
-pip install -e .
-```
-
-The installation should not take longer than a few seconds (depending on your internet connection).
-
-To use the notebooks, also install jupyter:
-    
-```bash
-pip install jupyter
-```
-
-## Usage
-
-Fucci phase currently supports loading a 
-[TrackMate](https://imagej.net/plugins/trackmate/) XML file:
-
-```python
-from fucciphase import process_trackmate
-from fucciphase.sensor import get_fuccisa_default_sensor
-
-trackmate_xml = "path/to/trackmate.xml"
-channel1 = "MEAN_INTENSITY_CH3"
-channel2 = "MEAN_INTENSITY_CH4"
-
-sensor = get_fuccisa_default_sensor()
-
-df = process_trackmate(trackmate_xml,
-                       channels=[channel1, channel2],
-		       sensor=sensor,
-                       thresholds=[0.1, 0.1])
-print(df)
-```
-
-The TrackMate XML is converted to a [Pandas](https://pandas.pydata.org/) DataFrame.
-Thus, in general data (e.g., stored in a CSV or XLSX file) that can be parsed into
-a DataFrame is supported.
-
-Have a look at the examples in the `example` folder to get more information!
-
-The runtime of the scripts depends on your datasize. 2D samples with a few hundred to a few thousand cells
-can be processed in a few minutes. Visualization in Napari can take a bit longer.
-Standard processing does not require a powerful computer.
-Make sure that you have sufficient RAM to load videos for visualization in Napari.
-
-## Development
-
-To develop fucciphase, clone the repository, install fucciphase in your environment
-and install the pre-commit hooks:
-
-```bash
-git clone https://github.com/Synthetic-Physiology-Lab/fucciphase
-cd fucciphase
-pip install -e ".[test, dev]"
-pre-commit install
-```
-
-If you want to build the documentation, replace the abovementioned pip install by:
-```bash
-pip install -e ".[test, dev, doc]"
-```
-
-## Cite us
-
-Di Sante, M., Pezzotti, M., Zimmermann, J., Enrico, A., Deschamps, J., Balmas, E.,
-Becca, S., Solito, S., Reali, A., Bertero, A., Jug, F. and Pasqualini, F.S., 2025.
-CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies.
-bioRxiv, https://doi.org/10.1101/2024.12.19.629259 

fucciphase-0.0.2.dist-info/RECORD

@@ -1,24 +0,0 @@
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-fucciphase/fucci_phase.py,sha256=VgydHVN0nWzC6Eeh0LRaPHdScL2w7C5X7IhGSvyp4qw,6134
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