fucciphase 0.0.1__py3-none-any.whl → 0.0.2__py3-none-any.whl

fucciphase/main_cli.py

@@ -0,0 +1,200 @@
+import argparse
+import json
+
+import pandas as pd
+
+from fucciphase import process_dataframe, process_trackmate
+from fucciphase.napari import add_trackmate_data_to_viewer
+from fucciphase.phase import estimate_percentage_by_subsequence_alignment
+from fucciphase.sensor import FUCCISASensor, get_fuccisa_default_sensor
+
+try:
+    import napari
+except ImportError as err:
+    raise ImportError("Install napari.") from err
+
+
+def main_cli() -> None:
+    """Fucciphase CLI."""
+    parser = argparse.ArgumentParser(
+        prog="fucciphase",
+        description="FUCCIphase tool to estimate cell cycle phases and percentages.",
+        epilog="Please report bugs and errors on GitHub.",
+    )
+    parser.add_argument("tracking_file", type=str, help="TrackMate XML or CSV file")
+    parser.add_argument(
+        "-ref",
+        "--reference_file",
+        type=str,
+        help="Reference cell cycle CSV file",
+        required=True,
+    )
+    parser.add_argument(
+        "--sensor_file",
+        type=str,
+        help="sensor file in JSON format "
+        "(can be skipped, then FUCCI SA sensor is used by default)",
+        default=None,
+    )
+    parser.add_argument(
+        "-dt", "--timestep", type=float, help="timestep in hours", required=True
+    )
+    parser.add_argument(
+        "-m",
+        "--magenta_channel",
+        type=str,
+        help="Name of magenta channel in TrackMate file",
+        required=True,
+    )
+    parser.add_argument(
+        "-c",
+        "--cyan_channel",
+        type=str,
+        help="Name of cyan channel in TrackMate file",
+        required=True,
+    )
+    parser.add_argument(
+        "--generate_unique_tracks",
+        type=bool,
+        help="Split subtracks (TrackMate specific)",
+        default=False,
+    )
+
+    args = parser.parse_args()
+
+    reference_df = pd.read_csv(args.reference_file)
+    reference_df.rename(
+        columns={"cyan": args.cyan_channel, "magenta": args.magenta_channel},
+        inplace=True,
+    )
+
+    if args.sensor_file is not None:
+        with open(args.sensor_file) as fp:
+            sensor_properties = json.load(fp)
+        sensor = FUCCISASensor(**sensor_properties)
+    else:
+        sensor = get_fuccisa_default_sensor()
+
+    if args.tracking_file.endswith(".xml"):
+        df = process_trackmate(
+            args.tracking_file,
+            channels=[args.cyan_channel, args.magenta_channel],
+            sensor=sensor,
+            thresholds=[0.1, 0.1],
+            generate_unique_tracks=args.generate_unique_tracks,
+        )
+    elif args.tracking_file.endswith(".csv"):
+        df = pd.read_csv(args.tracking_file)
+        process_dataframe(
+            df,
+            channels=[args.cyan_channel, args.magenta_channel],
+            sensor=sensor,
+            thresholds=[0.1, 0.1],
+            generate_unique_tracks=args.generate_unique_tracks,
+        )
+    else:
+        raise ValueError("Tracking file must be an XML or CSV file.")
+
+    track_id_name = "UNIQUE_TRACK_ID"
+    if not args.generate_unique_tracks:
+        track_id_name = "TRACK_ID"
+
+    estimate_percentage_by_subsequence_alignment(
+        df,
+        dt=args.timestep,
+        channels=[args.cyan_channel, args.magenta_channel],
+        reference_data=reference_df,
+        track_id_name=track_id_name
+    )
+    df.to_csv(args.tracking_file + "_processed.csv", index=False)
+
+
+def main_visualization() -> None:
+    """Fucciphase visualization."""
+    parser = argparse.ArgumentParser(
+        prog="fucciphase-napari",
+        description="FUCCIphase napari script to launch visualization.",
+        epilog="Please report bugs and errors on GitHub.",
+    )
+    parser.add_argument("fucciphase_file", type=str, help="Processed file.")
+    parser.add_argument(
+        "video", type=str, help="OME-Tiff file with video data and segmentation masks"
+    )
+    parser.add_argument(
+        "-m",
+        "--magenta_channel",
+        type=int,
+        help="Index of magenta channel in video file",
+        required=True,
+    )
+    parser.add_argument(
+        "-c",
+        "--cyan_channel",
+        type=int,
+        help="Index of cyan channel in video file",
+        required=True,
+    )
+    parser.add_argument(
+        "-s",
+        "--segmask_channel",
+        type=int,
+        help="Index of segmentation mask channel in video file",
+        required=True,
+    )
+    parser.add_argument(
+            "--pixel_size",
+            type=float,
+            help="Pixel size, only used if not in metadata",
+            default=None)
+
+    args = parser.parse_args()
+
+    AICSIMAGE = False
+    BIOIMAGE = False
+    try:
+        from aicsimageio import AICSImage
+
+        AICSIMAGE = True
+    except ImportError as err:
+        from bioio import BioImage
+
+        BIOIMAGE = True
+        import bioio_ome_tiff
+
+        if not BIOIMAGE:
+            raise ImportError(
+                "Please install AICSImage or bioio to read videos"
+            ) from err
+    if AICSIMAGE:
+        image = AICSImage(args.video)
+    elif BIOIMAGE:
+        image = BioImage(args.video, reader=bioio_ome_tiff.Reader)
+    scale = (image.physical_pixel_sizes.Y, image.physical_pixel_sizes.X)
+    if None in scale:
+        if args.pixel_size is not None:
+            scale = (args.pixel_size, args.pixel_size)
+        else:
+            print("WARNING: No pixel sizes found, using unit scale")
+            scale = (1.0, 1.0)
+    cyan = image.get_image_dask_data("TYX", C=args.cyan_channel)
+    magenta = image.get_image_dask_data("TYX", C=args.magenta_channel)
+    masks = image.get_image_dask_data("TYX", C=args.segmask_channel)
+    track_df = pd.read_csv(args.fucciphase_file)
+
+    viewer = napari.Viewer()
+
+    add_trackmate_data_to_viewer(
+        track_df,
+        viewer,
+        scale=scale,
+        image_data=[cyan, magenta],
+        colormaps=["cyan", "magenta"],
+        labels=masks,
+        cycle_percentage_id="CELL_CYCLE_PERC_DTW",
+        textkwargs={"size": 14},
+    )
+    napari.run()
+
+
+if __name__ == "__main__":
+    main_cli()

fucciphase/plot.py

@@ -293,7 +293,7 @@ def plot_dtw_query_vs_reference(
             "Percentage column not found in reference DataFrame"
             f", available options {reference_df.columns}"
         )
-    fig, ax = plt.subplots(1, len(channels))
+    _, ax = plt.subplots(1, len(channels))
     for idx, channel in enumerate(channels):
         ax[idx].plot(
             df[est_percentage_column], df[channel], label="Query", **plot_kwargs
@@ -540,7 +540,7 @@ def plot_cell_trajectory(
                 **kwargs,
             )
         )
-    fig, ax = plt.subplots()
+    _, ax = plt.subplots()
     for line_collection in line_collections:
         ax.add_collection(line_collection)
     ax.margins(0.05)

{fucciphase-0.0.1.dist-info → fucciphase-0.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fucciphase
-Version: 0.0.1
+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
@@ -57,7 +57,7 @@ Obtain cell cycle information from FUCCI fluorescence intensities.
 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.
 
-(SOON) To install from pip:
+To install from pip:
 
 ```bash
 pip install fucciphase

{fucciphase-0.0.1.dist-info → fucciphase-0.0.2.dist-info}/RECORD

@@ -1,8 +1,9 @@
 fucciphase/__init__.py,sha256=8PA6UNaYjycfPpOg7e5ArP3k9Lj9H15Lmw-Mnd14azY,375
 fucciphase/fucci_phase.py,sha256=VgydHVN0nWzC6Eeh0LRaPHdScL2w7C5X7IhGSvyp4qw,6134
 fucciphase/io.py,sha256=ELcoxsPHzcg9tf48MaMNnuSMxe0Fd3Nc9LCWbQ6p4I8,1715
+fucciphase/main_cli.py,sha256=S4nRitMkLFFR77DHDT3j5_OtYbTST55ysMzE9J8pf9I,5979
 fucciphase/phase.py,sha256=jy2l9LD81FTk6TIlyWyYPbVnwClGP9N4RrYyqtiMStg,17130
-fucciphase/plot.py,sha256=Obfv2VOHdDN4Az_JUErJ22ESAgHhdsBaavdsS0f6xZ4,18593
+fucciphase/plot.py,sha256=gFoprFvJGH5Zb-227riRH1x5NEAAhpeqaVCyb1kYLr8,18589
 fucciphase/py.typed,sha256=esB4cHc6c07uVkGtqf8at7ttEnprwRxwk8obY8Qumq4,187
 fucciphase/sensor.py,sha256=6-WEI8viI5fSVyKHnECmKYKaROW4tQaPaNW4hHYVAcA,14788
 fucciphase/tracking_utilities.py,sha256=IfKH2fyPo7fkW3PBvQrCz-UcfrdkOj7D-iLJabynvfw,2776
@@ -16,7 +17,8 @@ fucciphase/utils/phase_fit.py,sha256=Ht_dEyuLYonv6is9qQ-Xd95pQR7IR-8C8mv0ckDcp4E
 fucciphase/utils/simulator.py,sha256=7bmrO0IWUqsk4CyM-PlVpG2QTJxjTsY1h6buxmTs1iM,2322
 fucciphase/utils/track_postprocessing.py,sha256=cTe3OOCR4dxFBZwN7XdbzDbnsgouoJql8rv4WwvmbM8,14438
 fucciphase/utils/trackmate.py,sha256=dir4ayS1Fl-gtK8NTbP7t7CBLnrumC8LgPiCwxsBf-c,10666
-fucciphase-0.0.1.dist-info/METADATA,sha256=TL-dyIUGTeLdahG5YiQiWhq3i8o3esSpvujY47rLP14,4900
-fucciphase-0.0.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-fucciphase-0.0.1.dist-info/licenses/LICENSE,sha256=pQGrOGpOTwikEzkZ8Zc9XLQwbaZ85TMJP-GaWCNZciw,1554
-fucciphase-0.0.1.dist-info/RECORD,,
+fucciphase-0.0.2.dist-info/METADATA,sha256=Hbprshl_yGXUkarqCfjd1r34CDz9doj2HSHo5XN0m8Q,4893
+fucciphase-0.0.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+fucciphase-0.0.2.dist-info/entry_points.txt,sha256=B77Cm5QnxeQz6DEfqD6n7zDw48-HrlepWPwLbdVITMY,119
+fucciphase-0.0.2.dist-info/licenses/LICENSE,sha256=pQGrOGpOTwikEzkZ8Zc9XLQwbaZ85TMJP-GaWCNZciw,1554
+fucciphase-0.0.2.dist-info/RECORD,,

fucciphase-0.0.2.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+fucciphase = fucciphase.main_cli:main_cli
+fucciphase-napari = fucciphase.main_cli:main_visualization