Merge pull request #16 from imcf/shading

Add `simple_flatfield_correction()` to `shading` module

Author: ehrenfeu

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 +181,38 @@ 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.
+
+    The function returns a 32-bit corrected flatfield image.
+
+    Parameters
+    ----------
+    imp : ij.ImagePlus
+        The input stack to be projected.
+    sigma: float, optional
+        The sigma value for the Gaussian blur, default=20.0
+
+    Returns
+    -------
+    ij.ImagePlus
+        The 32-bit image result of flatfield correction
+
+    """
+    flatfield = imp.duplicate()
+    sigma_str = "sigma=" + str(sigma)
+
+    IJ.run(flatfield, "Gaussian Blur...", sigma_str)
+    stats = StackStatistics(flatfield)
+
+    # Normalize image to the highest value of original (requires 32-bit image)
+    IJ.run(flatfield, "32-bit", "")
+    IJ.run(
+        flatfield,
+        "Divide...",
+        "value=" + str(stats.max))
+    ic = ImageCalculator()
+    flatfield_corrected = ic.run("Divide create", imp, flatfield)
+
+    return flatfield_corrected

tests/imagej/shading-test.md

@@ -0,0 +1,18 @@
+### ----------------------
+
+ The following code block is a `python` script to be used in a Fiji with the shading branch's .jar already pasted into ./jars in the Fiji installation
+
+ Recommended is to import an image you wish to test on (Shaded-blobs.png e.g) and then drag this script into Fiji and run it.
+ If a resulting image pops up (while using flatfield method), everything works finely.
+### ----------------------
+
+```python
+from imcflibs.imagej import shading
+# import imcflibs.imagej
+import ij
+from ij import IJ
+
+imp = IJ.getImage()
+imcf_shading = shading.simple_flatfield_correction(imp)
+# Or any other method in class shading
+imcf_shading.show()