Add imagej.projections.project_stack()

pyproject.toml

@@ -21,7 +21,7 @@ version = "0.0.0"
 # - or: python = ">=3.10"
 
 [tool.poetry.dependencies]
-imcf-fiji-mocks = ">=0.6.0"
+imcf-fiji-mocks = ">=0.7.0"
 python = ">=2.7"
 python-micrometa = "^15.2.2"
 sjlogging = ">=0.5.2"

src/imcflibs/imagej/projections.py

@@ -1,13 +1,18 @@
-"""Functions for creating Z projections."""
+"""Functions for creating projections."""
 
 from ij.plugin import ZProjector  # pylint: disable-msg=E0401
 
 from .bioformats import export_using_orig_name  # pylint: disable-msg=E0401
 from ..log import LOG as log
 
+from net.imagej.axis import Axes
+from net.imagej.ops import Ops
+from ij import ImagePlus, IJ
+from net.imagej import Dataset
+
 
 def average(imp):
-    """Create an average intensity projection.
+    """Create an average intensity Z projection.
 
     Parameters
     ----------
@@ -23,13 +28,13 @@
         log.warn("ImagePlus is not a z-stack, not creating a projection!")
         return imp
 
-    log.debug("Creating average projection...")
+    log.debug("Creating average Z projection...")
     proj = ZProjector.run(imp, "avg")
     return proj
 
 
 def maximum(imp):
-    """Create a maximum intensity projection.
+    """Create a maximum intensity Z projection.
 
     Parameters
     ----------
@@ -45,7 +50,7 @@
         log.warn("ImagePlus is not a z-stack, not creating a projection!")
         return imp
 
-    log.debug("Creating maximum intensity projection...")
+    log.debug("Creating maximum intensity Z projection...")
     proj = ZProjector.run(imp, "max")
     return proj
 
@@ -100,3 +105,77 @@
         proj.close()
 
     return True
+
+
+def project_stack(imp, projected_dimension, projection_type, ops, ds, cs):
+    """Project along a defined axis using the given projection type.
+
+    Parameters
+    ----------
+    imp : ImagePlus
+        The input image to be projected.
+    projected_dimension : str
+        The dimension along which to project the data. Must be one of {"X", "Y", "Z",
+        "TIME", "CHANNEL"}.
+    projection_type : str
+        The type of projection to perform. Must be one of {"Max", "Mean", "Median",
+        "Min", "StdDev", "Sum"}.
+    ops : OpService
+        The service used to access image processing operations. Use e.g. from script
+        parameter: `#@ OpService ops`
+    ds : DatasetService
+        The service used to create new datasets. Use e.g. from script parameter:
+        `#@ DatasetService ds`
+    cs : ConvertService
+        The service used to convert between formats. Use e.g. from script parameter:
+        `#@ ConvertService cs`
+
+    Returns
+    -------
+    ImagePlus
+        The resulting projected image as an ImagePlus object.
+
+    Raises
+    ------
+    Exception
+        If the specified dimension is not found or if the dimension has only one frame.
+    """
+    bit_depth = imp.getBitDepth()
+    data = cs.convert(imp, Dataset)
+    # Select which dimension to project
+    dim = data.dimensionIndex(getattr(Axes, projected_dimension))
+    if dim == -1:
+        raise Exception("%s dimension not found." % projected_dimension)
+    if data.dimension(dim) < 2:
+        raise Exception("%s dimension has only one frame." % projected_dimension)
+
+    # Write the output dimensions
+    new_dimensions = [
+        data.dimension(d) for d in range(0, data.numDimensions()) if d != dim
+    ]
+
+    # Create the output image
+    projected = ops.create().img(new_dimensions)
+
+    # Create the op and run it
+    proj_op = ops.op(getattr(Ops.Stats, projection_type), data)
+    ops.transform().project(projected, data, proj_op, dim)
+
+    # Create the output Dataset and convert to ImagePlus
+    output = ds.create(projected)
+    output_imp = cs.convert(output, ImagePlus)
+    output_imp = output_imp.duplicate()
+    output_imp.setTitle("%s %s projection" % (projected_dimension, projection_type))
+    IJ.run(output_imp, "Enhance Contrast", "saturated=0.35")
+
+    # Rescale bit depth if possible
+    if projection_type in ["Max", "Min", "Median"]:
+        IJ.run("Conversions...", " ")
+        if bit_depth in [8, 16]:
+            IJ.run(output_imp, str(bit_depth) + "-bit", "")
+        if bit_depth == 12:
+            IJ.run(output_imp, "16-bit", "")
+
+        IJ.run("Conversions...", "scale")
+
+    return output_imp