From 5a97a7b8314e21ad21402c5fb7ef4a2936a66bd1 Mon Sep 17 00:00:00 2001 From: "kai.schleicher@unibas.ch" Date: Mon, 18 Aug 2025 10:43:15 +0200 Subject: [PATCH 1/3] Fix function to not split time points by default --- src/imcflibs/imagej/bdv.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/imcflibs/imagej/bdv.py b/src/imcflibs/imagej/bdv.py index 5cc7b412..af592c8f 100644 --- a/src/imcflibs/imagej/bdv.py +++ b/src/imcflibs/imagej/bdv.py @@ -846,6 +846,12 @@ def define_dataset_auto( hdf5_chunk_sizes = "hdf5_chunk_sizes=" + hdf5_chunk_sizes + " " else: hdf5_chunk_sizes = "" + if timepoints_per_partition > 0: + split_timepoints = "split_hdf5 timepoints_per_partition=" + str( + timepoints_per_partition + ) + else: + split_timepoints = "" if bf_series_type == "Angles": angle_rotation = "apply_angle_rotation " @@ -883,9 +889,7 @@ def define_dataset_auto( + angle_rotation + subsampling_factors + hdf5_chunk_sizes - + "split_hdf5 " - + "timepoints_per_partition=" - + str(timepoints_per_partition) + + split_timepoints + " " + "setups_per_partition=0 " + "use_deflate_compression " From adfb659874aef4ebd4746470e585fdcce8c65754 Mon Sep 17 00:00:00 2001 From: Kai Schleicher Date: Wed, 14 Jan 2026 15:16:36 +0100 Subject: [PATCH 2/3] Set default timepoints per partition to 0 --- src/imcflibs/imagej/bdv.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/imcflibs/imagej/bdv.py b/src/imcflibs/imagej/bdv.py index af592c8f..75904b3a 100644 --- a/src/imcflibs/imagej/bdv.py +++ b/src/imcflibs/imagej/bdv.py @@ -789,7 +789,7 @@ def define_dataset_auto( file_path, bf_series_type, dataset_save_path=None, - timepoints_per_partition=1, + timepoints_per_partition=0, resave="Re-save as multiresolution HDF5", subsampling_factors=None, hdf5_chunk_sizes=None, From 60d87565aca99cc61ee0b475d9928ca7481492af Mon Sep 17 00:00:00 2001 From: Kai Schleicher Date: Wed, 14 Jan 2026 15:17:16 +0100 Subject: [PATCH 3/3] Clarify file splitting behavior in the docstring --- src/imcflibs/imagej/bdv.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/imcflibs/imagej/bdv.py b/src/imcflibs/imagej/bdv.py index 75904b3a..88553892 100644 --- a/src/imcflibs/imagej/bdv.py +++ b/src/imcflibs/imagej/bdv.py @@ -812,8 +812,9 @@ def define_dataset_auto( Defines how Bio-Formats interprets the series. timepoints_per_partition : int, optional Split the output dataset by timepoints. Use `0` for no split, resulting - in a single HDF5 file containing all timepoints. By default `1`, - resulting in a HDF5 per timepoints. + in a single HDF5 file containing all timepoints. Otherwise, choose the + number of timepoints per file. By default `0`. + resave : str, optional Allow the function to either re-save the images or simply create a merged xml. Use `Load raw data` to avoid re-saving, by default `Re-save