From f29a57b57198184a35f08e68e81f607e9d391d12 Mon Sep 17 00:00:00 2001
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch>
Date: Mon, 17 Dec 2018 22:51:36 +0100
Subject: [PATCH] Add imagej.projections module for doing stack projections
---
src/imcflibs/imagej/projections.py | 73 ++++++++++++++++++++++++++++++
1 file changed, 73 insertions(+)
create mode 100644 src/imcflibs/imagej/projections.py
diff --git a/src/imcflibs/imagej/projections.py b/src/imcflibs/imagej/projections.py
new file mode 100644
index 0000000..c25107c
--- /dev/null
+++ b/src/imcflibs/imagej/projections.py
@@ -0,0 +1,73 @@
+"""Functions for creating Z projections."""
+
+from .bioformats import export_using_orig_name
+
+from ij.plugin import ZProjector
+
+
+def average(imp):
+ """Create an average intensity projection.
+
+ Parameters
+ ----------
+ imp : ij.ImagePlus
+ The input stack to be projected.
+
+ Returns
+ -------
+ ij.ImagePlus
+ The result of the projection.
+ """
+ # log.debug("Creating average projection...")
+ proj = ZProjector.run(imp, "avg")
+ return proj
+
+
+def maximum(imp):
+ """Create a maximum intensity projection.
+
+ Parameters
+ ----------
+ imp : ij.ImagePlus
+ The input stack to be projected.
+
+ Returns
+ -------
+ ij.ImagePlus
+ The result of the projection.
+ """
+ # log.debug("Creating maximum intensity projection...")
+ proj = ZProjector.run(imp, "max")
+ return proj
+
+
+def create_and_save(imp, projections, path, filename, export_format):
+ """Wrapper to create one or more projections and export the results.
+
+ Parameters
+ ----------
+ imp : ij.ImagePlus
+ The image stack to create the projections from.
+ projections : list(str)
+ A list of projection types to be done, valid options are 'Average',
+ 'Maximum' and 'Sum'.
+ path : str
+ The path to store the results in.
+ filename : str
+ The original file name to derive the results name from.
+ export_format : str
+ The suffix to be given to Bio-Formats, determining the storage format.
+ """
+ command = {
+ 'Average': 'avg',
+ 'Maximum': 'max',
+ 'Sum': 'sum',
+ }
+ for projection in projections:
+ # log.debug("Creating '%s' projection..." % projection)
+ proj = ZProjector.run(imp, command[projection])
+ export_using_orig_name(proj,
+ path, filename,
+ "-%s" % command[projection],
+ export_format)
+ proj.close()
--
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