From 5dde41f8446eb2399db0f0c16e29f6bb1146937f Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Mon, 18 Feb 2019 16:48:48 +0100
Subject: [PATCH] Add 'imagej.split' module
---
src/imcflibs/imagej/split.py | 44 ++++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
create mode 100644 src/imcflibs/imagej/split.py
diff --git a/src/imcflibs/imagej/split.py b/src/imcflibs/imagej/split.py
new file mode 100644
index 0000000..8aa15b0
--- /dev/null
+++ b/src/imcflibs/imagej/split.py
@@ -0,0 +1,44 @@
+"""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)
--
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