Add imagej.projections module for doing stack projections

src/imcflibs/imagej/projections.py

+"""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()