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2 changes: 1 addition & 1 deletion scripts/script_cropped_fov.py
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
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)
# exclusive upper bound on frames to load (tmax=66 loads frames 0–65), defaults to None (use all frames)
tmax = 66
# (Z),Y,X, defaults to (1, 1, 1)
scale = (0.1494, 0.1494)
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2 changes: 1 addition & 1 deletion scripts/script_instanseg.py
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
)
# 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)
# exclusive upper bound on frames to load (tmax=100 loads frames 0–99), defaults to None (use all frames)
tmax = 100
# (Z),Y,X, defaults to (1, 1, 1)
scale = (1.625, 0.40625, 0.40625)
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2 changes: 1 addition & 1 deletion scripts/script_neuromast.py
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@
)
# 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)
# exclusive upper bound on frames to load (tmax=600 loads frames 0–599), defaults to None (use all frames)
tmax = 600
# (Z),Y,X, defaults to (1, 1, 1)
scale = (0.25, 0.108, 0.108) # microns
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4 changes: 2 additions & 2 deletions trackedit/DatabaseHandler.py
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ def __init__(
self,
db_filename_old: str,
working_directory: Path,
Tmax: int,
Tmax: int, # exclusive upper bound: Tmax=10 loads frames 0–9
scale: tuple,
name: str,
annotation_mapping: dict = None,
Expand Down Expand Up @@ -556,7 +556,7 @@ def check_if_tmax_changed(self):
# If max time is less than current Tmax, update it
if (
current_max_time < self.Tmax - 1
): # Tmax of 600 means 599 is the last timepoint
): # Tmax is exclusive: Tmax=600 loads frames 0–599
self.Tmax = current_max_time
(
self.time_window,
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2 changes: 1 addition & 1 deletion trackedit/run.py
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ def run_trackedit(
Args:
working_directory: Path to working directory
db_filename: Name of database file
tmax: Maximum time point
tmax: Exclusive upper bound on time points to load (e.g. tmax=10 loads frames 0–9)
scale: Scale factors for each dimension
name: Name for the tracks layer
time_chunk: Starting time chunk
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4 changes: 4 additions & 0 deletions trackedit/utils/utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -260,6 +260,10 @@ def solution_dataframe_from_sql_with_tmax(
database_path : str
SQL database path (e.g. sqlite:///your.database.db)

tmax : int
Exclusive upper bound on time points to load. Nodes with t >= tmax are excluded
(e.g. tmax=10 loads frames 0–9).

columns : Sequence[sqla.Column], optional
Queried columns, MUST include NodeDB.id.
By default (NodeDB.id, NodeDB.parent_id, NodeDB.t, NodeDB.z, NodeDB.y, NodeDB.x)
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