Merge pull request #108 from CellKai/modify-bf-import

Add option to crop region

Author: ehrenfeu

src/imcflibs/imagej/_loci.py

@@ -24,15 +24,18 @@
 ### *** WARNING *** ### *** WARNING *** ### *** WARNING *** ### *** WARNING ***
 #
 
-
+# unproblematic imports kept here for consistency
 from loci.plugins import BF
+from loci.common import Region
+from loci.formats import ImageReader, Memoizer, MetadataTools
 
 # dummy objects to prevent failing imports in a non-ImageJ / Jython context:
 ImporterOptions = None
 ZeissCZIReader = None
 DefaultMetadataOptions = None
 MetadataLevel = None
 DynamicMetadataOptions = None
+MetadataOptions = None
 
 # perform the actual imports when running under Jython using `importlib` calls:
 import platform as _python_platform
@@ -50,5 +53,3 @@
     DynamicMetadataOptions = _loci_formats_in.DynamicMetadataOptions
     MetadataOptions = _loci_formats_in.MetadataOptions
 del _python_platform
-
-from loci.formats import ImageReader, Memoizer, MetadataTools

src/imcflibs/imagej/bioformats.py

@@ -24,6 +24,7 @@
     Memoizer,
     MetadataTools,
     ZeissCZIReader,
+    Region,
 )
 
 
@@ -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.
 
@@ -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
     -------
@@ -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))