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17 changes: 11 additions & 6 deletions src/imcflibs/imagej/bdv.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand All @@ -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
Expand Down Expand Up @@ -846,6 +847,12 @@ 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 "
Expand Down Expand Up @@ -883,9 +890,7 @@ 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 "
Expand Down
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