Add 'imagej.split' module

src/imcflibs/imagej/split.py

+"""Functions for splitting channels and or slices."""
+
+import os
+
+from ij import IJ, ImagePlus  # pylint: disable-msg=E0401
+from ij.io import FileSaver  # pylint: disable-msg=E0401
+from ij.plugin import ChannelSplitter  # pylint: disable-msg=E0401
+
+def split_by_c_and_z(log, dname, imgf, skip_top, skip_bottom):
+    """Helper function to open, split and save a file.
+
+    Load the file specified, split by channels and z-slices, create a directory
+    for each channel using the channel number as a name suffix and export
+    each slice as an individual TIF file.
+
+    Parameters
+    ----------
+    log : logger or scijava-logservice
+        The logger object to be used for logging.
+    dname : str
+        The directory to load TIF files from.
+    imgf : str
+        The file name to load and split.
+    skip_top : int
+        Number of slices to skip at the top.
+    skip_bottom : int
+        Number of slices to skip at the bottom.
+    """
+    log.info("Processing file [%s]" % imgf)
+    imp = IJ.openImage(dname + "/" + imgf)
+    fname = os.path.splitext(imgf)
+    channels = ChannelSplitter().split(imp)
+    for channel in channels:
+        c_name = channel.getTitle().split("-")[0]
+        tgt_dir = os.path.join(dname, fname[0] + "-" + c_name)
+        if not os.path.isdir(tgt_dir):
+            os.mkdir(tgt_dir)
+        stack = channel.getStack()
+        for z in range(1+skip_top, stack.getSize()+1-skip_bottom):
+            proc = stack.getProcessor(z)
+            fout = "%s/%s-z%s%s" % (tgt_dir, fname[0], z, fname[1])
+            # fout = dname + "/" + c_name + "/" + fname[0] + "-z" + z + fname[1]
+            log.info("Writing channel %s, slice %s: %s" % (c_name, z, fout))
+            FileSaver(ImagePlus(fname[0], proc)).saveAsTiff(fout)