partial annotation of tracks (#71)

* partial annotation of tracks

* forgot to save last changes

* removed ziwens script, which was outdated

* Organelle-Dynamics branch (#72)

* organelle-dynamics-branch

* revert neuromast path back to default

* added default value

* pre-commit fixes

* renamed Ziwens script

* bump version to 0.0.6

Author: TeunHuijben

scripts/script_cropped_fov.py

@@ -0,0 +1,83 @@
+import operator
+import sys
+import warnings
+from pathlib import Path
+
+import numpy as np
+from ultrack.core.database import NodeDB
+
+from trackedit.run import run_trackedit
+
+# Databases saved with numpy>2 need np._core.numeric, which is not available in numpy<2, hence the following hack
+sys.modules["numpy._core.numeric"] = np.core.numeric
+
+warnings.filterwarnings("ignore", category=FutureWarning, message=".*qt_viewer.*")
+
+# **********INPUTS*********
+# path to the working directory that contains the database file AND metadata.toml:
+working_directory = Path("/home/teun.huijben/Documents/data/Ziwen/2025_07_24_A549/")
+# name of the database file to start from, or "latest" to start from the latest version, defaults to "data.db"
+db_filename_start = "latest"
+# maximum number of frames display, defaults to None (use all frames)
+tmax = 66
+# (Z),Y,X, defaults to (1, 1, 1)
+scale = (0.1494, 0.1494)
+# overwrite existing database/changelog, defaults to False (not used when db_filename_start is "latest")
+allow_overwrite = False
+
+# OPTIONAL: imaging data
+imaging_zarr_file = (
+    "/hpc/projects/intracellular_dashboard/organelle_dynamics/rerun/"
+    "2025_07_24_A549_SEC61_TOMM20_G3BP1_ZIKV/2-assemble/"
+    "2025_07_24_A549_SEC61_TOMM20_G3BP1_ZIKV.zarr/A/1/000000/"
+)
+imaging_channel = "0"
+image_z_slice = (
+    20  # (only look at specific z-slice of 3D stack, because tracking data was 2D)
+)
+image_translate = (
+    0,
+    442 * 0.15,  # (taken from 2-assemble/concatenate_cropped.yml)
+    161 * 0.15,  # (taken from 2-assemble/concatenate_cropped.yml)
+)  # (t,y,x) because we use image_z_slice=20, so the z-axis is collapsed
+
+# imaging_zarr_file = None
+# imaging_channel = None
+# image_translate = None
+
+# OPTIONAL: annotation mapping (default is neuromast cell types)
+annotation_mapping = {
+    1: {"name": "normal", "color": [0.0, 1.0, 0.0, 1.0]},  # green
+    2: {"name": "infected", "color": [1.0, 0.0, 0.0, 1.0]},  # red
+    3: {"name": "other", "color": [0.5, 0.5, 0.5, 1.0]},  # grey
+}
+default_start_annotation = 1  # not-infected
+# annotation_mapping = None
+# default_start_annotation = None
+
+
+# filter the database segments on pixel coordinates
+# (if only displaying a crop of the full dataset)
+coordinate_filters = [
+    (NodeDB.x, operator.lt, 1280),  # lt = less than (<), coorddinates in db/pixel units
+    (NodeDB.x, operator.gt, 161),  # gt = greater than (>)
+    (NodeDB.y, operator.lt, 1186),
+    (NodeDB.y, operator.gt, 442),
+]
+# *************************
+
+if __name__ == "__main__":
+    run_trackedit(
+        working_directory=working_directory,
+        db_filename=db_filename_start,
+        tmax=tmax,
+        scale=scale,
+        allow_overwrite=allow_overwrite,
+        imaging_zarr_file=imaging_zarr_file,
+        imaging_channel=imaging_channel,
+        image_z_slice=image_z_slice,
+        image_translate=image_translate,
+        annotation_mapping=annotation_mapping,
+        coordinate_filters=coordinate_filters,
+        default_start_annotation=default_start_annotation,
+    )