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Add option to crop region #108

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Add option to crop region #108

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13 changes: 12 additions & 1 deletion src/imcflibs/imagej/bioformats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
Memoizer,
MetadataTools,
ZeissCZIReader,
Region,
)


Expand Down Expand Up @@ -186,6 +187,7 @@ def import_image(
t_start=None,
t_end=None,
t_interval=None,
region=None,
):
"""Open an image file using the Bio-Formats importer.

Expand Down Expand Up @@ -229,8 +231,11 @@ def import_image(
only import a subset of time points ending with this one. Requires to
set t_start and t_interval.
t_interval : int, optional
only import a subset of time points with thsi interval. Requires to set
only import a subset of time points with this interval. Requires to set
t_start and t_end.
region : list, optional
Bio-Formats crop region, by default None.
Format = [start_x, start_y, width in px, height in px]

Returns
-------
Expand Down Expand Up @@ -276,6 +281,12 @@ def import_image(
options.setTEnd(series_number, t_end)
options.setTStep(series_number, t_interval)

if region is not None:
options.setCrop(True)
options.setCropRegion(
series_number, Region(region[0], region[1], region[2], region[3])
)

log.info("Reading [%s]", filename)
orig_imps = BF.openImagePlus(options)
log.debug("Opened [%s] %s", filename, type(orig_imps))
Expand Down
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