Add imagej.bioformats module

src/imcflibs/imagej/bioformats.py

+"""Bio-Formats related helper functions.
+
+NOTE: this is *NOT* about using [python-bioformats][1] but rather about calling
+the corresponding functions provided by ImageJ.
+
+[1]: https://pypi.org/project/python-bioformats/
+
+"""
+
+import os
+
+from ij import IJ
+from loci.plugins import BF
+from loci.plugins.in import ImporterOptions
+
+from ..pathtools import image_basename
+
+
+def import_image(filename,
+                 color_mode='color',
+                 split_c=False, split_z=False, split_t=False):
+    """Open an image file using the Bio-Formats importer.
+
+    Parameters
+    ----------
+    filename : str
+        The full path to the file to be imported through Bio-Formats.
+    color_mode : str, optional
+        The color mode to be used for the resulting ImagePlus, one of 'color',
+        'composite', 'gray' and 'default'.
+    split_c : bool, optional
+        Whether to split the channels into separate ImagePlus objects.
+    split_z : bool, optional
+        Whether to split the z-slices into separate ImagePlus objects.
+    split_t : bool, optional
+        Whether to split the time points into separate ImagePlus objects.
+
+    Returns
+    -------
+    ij.ImagePlus[]
+        A list of ImagePlus objects resulting from the import.
+    """
+    options = ImporterOptions()
+    mode = {
+        'color' : ImporterOptions.COLOR_MODE_COLORIZED,
+        'composite' : ImporterOptions.COLOR_MODE_COMPOSITE,
+        'gray' : ImporterOptions.COLOR_MODE_GRAYSCALE,
+        'default' : ImporterOptions.COLOR_MODE_DEFAULT,
+    }
+    options.setColorMode(mode[color_mode])
+    options.setSplitChannels(split_c)
+    options.setSplitFocalPlanes(split_z)
+    options.setSplitTimepoints(split_t)
+    options.setId(filename)
+    # log.info("Reading [%s]" % filename)
+    orig_imps = BF.openImagePlus(options)
+    return orig_imps
+
+
+def export(imp, filename):
+    """Simple wrapper to export an image to a given file.
+
+    Parameters
+    ----------
+    imp : ImagePlus
+        The ImagePlus object to be exported by Bio-Formats.
+    filename : str
+        The output filename, may include a full path.
+    """
+    # log.info("Exporting to [%s]" % out_file)
+    IJ.run(imp, "Bio-Formats Exporter", "save=[" + filename + "]")
+    # log.debug("Exporting finished.")
+
+
+def export_using_orig_name(imp, path, orig_name, tag, suffix):
+    """Export an image to a given path, deriving the name from the input file.
+
+    The input filename is stripped to its pure file name, without any path or
+    suffix components, then an optional tag (e.g. "-avg") and the new format
+    suffix is added.
+
+    Parameters
+    ----------
+    imp : ImagePlus
+        The ImagePlus object to be exported by Bio-Formats.
+    path : str or object that can be cast to a str
+        The output path.
+    orig_name : str or object that can be cast to a str
+        The input file name, may contain arbitrary path components.
+    tag : str
+        An optional tag to be added at the end of the new file name, can be used
+        to denote information like "-avg" for an average projection image.
+    suffix : str
+        The new file name suffix, which also sets the file format for BF.    
+
+    Returns
+    -------
+    out_file : str
+        The full name of the exported file.
+    """
+    out_file = os.path.join(path, image_basename(orig_name) + tag + suffix)
+    export(imp, out_file)
+    return out_file