Merge branch 'code-kai-20230418' into devel

Author: ehrenfeu

src/imcflibs/imagej/bioformats.py

@@ -17,12 +17,28 @@
 
 from loci.plugins.in import ImporterOptions  # pdoc: skip
 
+from loci.formats import ImageReader, Memoizer
+
 from ..pathtools import gen_name_from_orig
 from ..log import LOG as log
 
 
 def import_image(
-    filename, color_mode="color", split_c=False, split_z=False, split_t=False
+    filename,
+    color_mode="color",
+    split_c=False,
+    split_z=False,
+    split_t=False,
+    series_number=None,
+    c_start=None,
+    c_end=None,
+    c_interval=None,
+    z_start=None,
+    z_end=None,
+    z_interval=None,
+    t_start=None,
+    t_end=None,
+    t_interval=None,
 ):
     """Open an image file using the Bio-Formats importer.
 
@@ -39,6 +55,35 @@ def import_image(
         Whether to split the z-slices into separate ImagePlus objects.
     split_t : bool, optional
         Whether to split the time points into separate ImagePlus objects.
+    series_number : int, optional
+        open a specific Bio-Formats series
+    c_start : int, optional
+        only import a subset of channel starting with this one. Requires to set
+        c_end and c_interval.
+    c_end : int, optional
+        only import channel(s) ending with this one. Requires to set c_start and
+        c_interval.
+    c_interval : int, optional
+        only import a subset of channel with this interval. Requires to set
+        c_start and c_end.
+    z_start : int, optional
+        only import a subset of planes starting with this one. Requires to set
+        z_end and z_interval.
+    z_end : int, optional
+        only import a subset of planes ending with this one. Requires to set
+        z_start and z_interval.
+    z_interval : int, optional
+        only import a subset of planes with this interval. Requires to set
+        z_start and z_end.
+    t_start : int, optional
+        only import a subset of time points starting with this one. Requires to
+        set t_end and t_interval.
+    t_end : int, optional
+        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
+        t_start and t_end.
 
     Returns
     -------
@@ -57,6 +102,33 @@ def import_image(
     options.setSplitFocalPlanes(split_z)
     options.setSplitTimepoints(split_t)
     options.setId(filename)
+    if series_number is not None:
+        options.setSeriesOn(series_number, True)
+
+    if c_start is not None:
+        if series_number is None:
+            series_number = 0
+        options.setSpecifyRanges(True)
+        options.setCBegin(series_number, c_start)
+        options.setCEnd(series_number, c_end)
+        options.setCStep(series_number, c_interval)
+
+    if z_start is not None:
+        if series_number is None:
+            series_number = 0
+        options.setSpecifyRanges(True)
+        options.setZBegin(series_number, z_start)
+        options.setZEnd(series_number, z_end)
+        options.setZStep(series_number, z_interval)
+
+    if t_start is not None:
+        if series_number is None:
+            series_number = 0
+        options.setSpecifyRanges(True)
+        options.setTBegin(series_number, t_start)
+        options.setTEnd(series_number, t_end)
+        options.setTStep(series_number, t_interval)
+
     log.info("Reading [%s]", filename)
     orig_imps = BF.openImagePlus(options)
     log.debug("Opened [%s] %s", filename, type(orig_imps))
@@ -131,3 +203,44 @@ def export_using_orig_name(imp, path, orig_name, tag, suffix, overwrite=False):
     out_file = gen_name_from_orig(path, orig_name, tag, suffix)
     export(imp, out_file, overwrite)
     return out_file
+
+
+def get_series_count_from_ome_metadata(path_to_file):
+    """Get the Bio-Formates series count from a file on disk.
+
+    Useful to access a specific image in a container format like .czi, .nd2, .lif...
+
+    Parameters
+    ----------
+    path_to_file : str
+        The full path to the image file.
+
+    Returns
+    -------
+    int
+        The number of Bio-Formats series detected in the image file metadata.
+    """
+    reader = ImageReader()
+    ome_meta = MetadataTools.createOMEXMLMetadata()
+    reader.setMetadataStore(ome_meta)
+    reader.setId(path_to_file)
+    series_count = reader.getSeriesCount()
+    reader.close()
+
+    return series_count
+
+
+def write_bf_memoryfile(path_to_file):
+    """Write a BF memo-file so subsequent access to the same file is faster.
+
+    The Bio-Formats memo-file is written next to the image file (i.e. in the
+    same folder as the given file).
+
+    Parameters
+    ----------
+    path_to_file : string
+        The full path to the image file.
+    """
+    reader = Memoizer(ImageReader())
+    reader.setId(path_to_file)
+    reader.close()

tests/imagej/bioformats/write_bf_memoryfile/test_01.py

@@ -0,0 +1,35 @@
+# @ File (label="Select the python-imcf-libs testdata directory", style="directory") PYTHON_IMCFLIBS_TESTDATA
+
+
+import os
+from imcflibs.pathtools import parse_path
+from imcflibs.imagej import bioformats
+
+
+components = parse_path("systems/lsm700/beads/10x_phmax.czi", PYTHON_IMCFLIBS_TESTDATA)
+full_path = components["full"]
+bfmemofile = components["path"] + "." + components["fname"] + ".bfmemo"
+
+if os.path.isfile(bfmemofile):
+    print("BF memory file [%s] already exists, removing..." % bfmemofile)
+    os.remove(bfmemofile)
+
+
+bioformats.write_bf_memoryfile(full_path)
+
+
+if not os.path.isfile(bfmemofile):
+    print("Test FAILED: can't find BF memory file [%s]" % bfmemofile)
+else:
+    print("Test passed, BF memory file [%s] was created." % bfmemofile)
+
+print(
+    """
+================================= IMPORTANT =================================
+Bio-Formats will only create a memory-file ONCE per session, meaning if this
+script is being run multiple times subsequently without closing ImageJ in
+between it will FAIL as the memory-file gets deleted by the script but will
+only be re-created by Bio-Formats in a FRESH ImageJ instance!!
+================================= IMPORTANT =================================
+"""
+)