Add method for simple flatfield correction

Author: rohangirishrao

src/imcflibs/imagej/shading.py

@@ -3,7 +3,9 @@
 import os
 
 import ij  # pylint: disable-msg=import-error
-
+from ij import IJ
+from ij.plugin import ImageCalculator, Concatenator
+from ij.process import StackStatistics, ImageProcessor
 from ..imagej import bioformats  # pylint: disable-msg=no-name-in-module
 from ..imagej import misc, projections
 from ..log import LOG as log
@@ -179,3 +181,29 @@ def process_files(files, outpath, model_file, fmt):
 
     if model:
         model.close()
+
+def simple_flatfield_correction(imp, sigma=20.0):
+    """
+    Performs a simple flatfield correction to a given ImagePlus stack and returns a 32-bit corrected flatfield image.
+    Parameters
+    ----------
+    imp : ij.ImagePlus
+        The input stack to be projected.
+    sigma: double, default 20.0
+        The sigma value for the Gaussian blur, default = 20.0
+    Returns
+    -------
+    ij.ImagePlus
+        The 32-bit image result of the flatfield correction
+
+    """
+    flatfield = imp.duplicate()
+    sigma_str = "sigma=" + str(sigma)
+    IJ.run(flatfield, "Gaussian Blur...", sigma_str) # Apply a gaussian blur
+    stats = StackStatistics(flatfield)
+    IJ.run(flatfield, "32-bit", "") # Make a 32 bit version of the image
+    IJ.run(flatfield, "Divide...", "value=" + str(stats.max)) # Normalize 32 bit image to the highest value of original
+    ic = ImageCalculator()
+    flatfield_corrected = ic.run("Divide create", imp, flatfield)
+
+    return flatfield_corrected