Merge pull request #143 from lguerard/rollingball_options

Additional options for rolling ball background subtraction

Author: ehrenfeu

src/imcflibs/imagej/processing.py

@@ -9,13 +9,77 @@
 from ..log import LOG as log
 
 
+def filter_options(filter_method, filter_radius, do_3d=False):
+    """Build the ImageJ filter command and options strings.
+
+    Parameters
+    ----------
+    filter_method : str
+        Name of the filter method to use. Must be one of:
+            - Median
+            - Mean
+            - Gaussian Blur
+            - Minimum
+            - Maximum
+    filter_radius : int
+        Radius of the filter to use.
+    do_3d : bool, optional
+        If set to True, will do a 3D filtering, by default False.
+
+    Returns
+    -------
+    tuple[str, str]
+        The filter name and options strings.
+    """
+
+    if do_3d:
+        filter_name = filter_method + " 3D..."
+    else:
+        filter_name = filter_method + "..."
+
+    if filter_method == "Gaussian Blur":
+        options = "sigma=" + str(filter_radius) + " stack"
+    else:
+        options = "radius=" + str(filter_radius) + " stack"
+
+    return filter_name, options
+
+
+def threshold_options(threshold_method, do_3d=True):
+    """Build the ImageJ threshold option strings.
+
+    Parameters
+    ----------
+    threshold_method : str
+        Name of the threshold method to use.
+    do_3d : bool, optional
+        If set to True, the automatic threshold will be done on a 3D stack,
+        by default True.
+
+    Returns
+    -------
+    tuple[str, str]
+        The auto threshold options and the convert to binary options strings.
+    """
+
+    auto_threshold_options = (
+        threshold_method + " " + "dark" + " " + "stack" if do_3d else ""
+    )
+
+    convert_to_binary_options = (
+        "method=" + threshold_method + " " + "background=Dark" + " " + "black"
+    )
+
+    return auto_threshold_options, convert_to_binary_options
+
+
 def apply_filter(imp, filter_method, filter_radius, do_3d=False):
     """Make a specific filter followed by a threshold method of choice.
 
     Parameters
     ----------
     imp : ImagePlus
-        Input ImagePlus to filter and threshold
+        Input ImagePlus to filter and threshold.
     filter_method : str
         Name of the filter method to use. Must be one of:
             - Median
@@ -24,16 +88,17 @@ def apply_filter(imp, filter_method, filter_radius, do_3d=False):
             - Minimum
             - Maximum
     filter_radius : int
-        Radius of the filter filter to use
+        Radius of the filter filter to use.
     do_3d : bool, optional
-        If set to True, will do a 3D filtering, by default False
+        If set to True, will do a 3D filtering, by default False.
 
 
     Returns
     -------
     ij.ImagePlus
-        Filtered ImagePlus
+        Filtered ImagePlus.
     """
+
     log.info("Applying filter %s with radius %d" % (filter_method, filter_radius))
 
     if filter_method not in [
@@ -47,16 +112,7 @@ def apply_filter(imp, filter_method, filter_radius, do_3d=False):
             "filter_method must be one of: Median, Mean, Gaussian Blur, Minimum, Maximum"
         )
 
-    if do_3d:
-        filter = filter_method + " 3D..."
-    else:
-        filter = filter_method + "..."
-
-    options = (
-        "sigma="
-        if filter_method == "Gaussian Blur"
-        else "radius=" + str(filter_radius) + " stack"
-    )
+    filter, options = filter_options(filter_method, filter_radius, do_3d=do_3d)
 
     log.debug("Filter: <%s> with options <%s>" % (filter, options))
 
@@ -66,69 +122,125 @@ def apply_filter(imp, filter_method, filter_radius, do_3d=False):
     return imageplus
 
 
-def apply_rollingball_bg_subtraction(imp, rolling_ball_radius, do_3d=False):
+def apply_rollingball_bg_subtraction(
+    imp,
+    rolling_ball_radius,
+    light_background=False,
+    sliding=False,
+    disable_smoothing=False,
+    do_3d=False,
+):
     """Perform background subtraction using a rolling ball method.
 
     Parameters
     ----------
     imp : ij.ImagePlus
-        Input ImagePlus to filter and threshold
+        Input ImagePlus to filter and threshold.
     rolling_ball_radius : int
-        Radius of the rolling ball filter to use
+        Radius of the rolling ball filter to use.
+    light_background : bool, optional
+        If set to True, will treat the background as light, by default False.
+    sliding : bool, optional
+        If set to True, will do a sliding window approach, by default False.
+    disable_smoothing : bool, optional
+        If set to True, will disable the smoothing, by default False.
     do_3d : bool, optional
-        If set to True, will do a 3D filtering, by default False
+        If set to True, will do a 3D filtering, by default False.
 
     Returns
     -------
     ij.ImagePlus
-        Filtered ImagePlus
+        Filtered ImagePlus.
     """
     log.info("Applying rolling ball with radius %d" % rolling_ball_radius)
 
-    options = "rolling=" + str(rolling_ball_radius) + " stack" if do_3d else ""
+    options = rolling_ball_options(
+        rolling_ball_radius,
+        light_background=light_background,
+        sliding=sliding,
+        disable_smoothing=disable_smoothing,
+        do_3d=do_3d,
+    )
 
     log.debug("Background subtraction options: %s" % options)
 
     imageplus = imp.duplicate()
-    IJ.run(imageplus, "Substract Background...", options)
+    IJ.run(imageplus, "Subtract Background...", options)
 
     return imageplus
 
 
+def rolling_ball_options(
+    rolling_ball_radius,
+    light_background=False,
+    sliding=False,
+    disable_smoothing=False,
+    do_3d=False,
+):
+    """Generate the options for the "Subtract Background..." macro command.
+
+    Parameters
+    ----------
+    rolling_ball_radius : int
+        Radius of the rolling ball filter to use.
+    light_background : bool, optional
+        If set to True, will treat the background as light, by default False.
+    sliding : bool, optional
+        If set to True, will do a sliding window approach, by default False.
+    disable_smoothing : bool, optional
+        If set to True, will disable the smoothing, by default False.
+    do_3d : bool, optional
+        If set to True, will do a 3D filtering, by default False.
+
+    Returns
+    -------
+    str
+        The options string for the "Subtract Background..." macro command.
+    """
+
+    parts = ["rolling=" + str(rolling_ball_radius)]
+    if light_background:
+        parts.append("light")
+    if sliding:
+        parts.append("sliding")
+    if disable_smoothing:
+        parts.append("disable")
+    if do_3d:
+        parts.append("stack")
+    return " ".join(parts)
+
+
 def apply_threshold(imp, threshold_method, do_3d=True):
     """Apply a threshold method to the input ImagePlus.
 
     Parameters
     ----------
     imp : ij.ImagePlus
-        Input ImagePlus to filter and threshold
+        Input ImagePlus to filter and threshold.
     threshold_method : str
-        Name of the threshold method to use
+        Name of the threshold method to use.
     do_3d : bool, optional
-        If set to True, the automatic threshold will be done on a 3D stack, by default True
+        If set to True, the automatic threshold will be done on a 3D stack,
+        by default True.
 
     Returns
     -------
     ij.ImagePlus
-        Thresholded ImagePlus
+        Thresholded ImagePlus.
     """
 
     log.info("Applying threshold method %s" % threshold_method)
 
     imageplus = imp.duplicate()
 
-    auto_threshold_options = (
-        threshold_method + " " + "dark" + " " + "stack" if do_3d else ""
+    auto_threshold_options, convert_to_binary_options = threshold_options(
+        threshold_method, do_3d=do_3d
     )
 
     log.debug("Auto threshold options: %s" % auto_threshold_options)
 
     IJ.setAutoThreshold(imageplus, auto_threshold_options)
 
-    convert_to_binary_options = (
-        "method=" + threshold_method + " " + "background=Dark" + " " + "black"
-    )
-
     log.debug("Convert to binary options: %s" % convert_to_binary_options)
 
     IJ.run(imageplus, "Convert to Mask", convert_to_binary_options)

tests/test_processing.py

@@ -0,0 +1,59 @@
+"""Tests for the imcflibs.imagej.processing module."""
+
+from imcflibs.imagej.processing import (
+    filter_options,
+    rolling_ball_options,
+    threshold_options,
+)
+
+
+def test_rolling_ball_options():
+    """Test the rolling_ball_options function."""
+
+    options = rolling_ball_options(42.23)
+    assert options == "rolling=42.23"
+
+
+def test_rolling_ball_options_with_flags():
+    """Test `rolling_ball_options()` string concatenation with all flags."""
+
+    options = rolling_ball_options(
+        12,
+        light_background=True,
+        sliding=True,
+        disable_smoothing=True,
+        do_3d=True,
+    )
+    assert options == "rolling=12 light sliding disable stack"
+
+
+def test_filter_options():
+    """Test `filter_options()` string concatenation."""
+
+    command, options = filter_options("Mean", 5, do_3d=True)
+    assert command == "Mean 3D..."
+    assert options == "radius=5 stack"
+
+
+def test_filter_options_gaussian_blur():
+    """Test `filter_options()` with the Gaussian Blur branch."""
+
+    command, options = filter_options("Gaussian Blur", 5)
+    assert command == "Gaussian Blur..."
+    assert options == "sigma=5 stack"
+
+
+def test_threshold_options():
+    """Test `threshold_options()` string concatenation."""
+
+    auto_threshold, convert_to_binary = threshold_options("Otsu", do_3d=True)
+    assert auto_threshold == "Otsu dark stack"
+    assert convert_to_binary == "method=Otsu background=Dark black"
+
+
+def test_threshold_options_without_stack():
+    """Test `threshold_options()` when 3D stacking is disabled."""
+
+    auto_threshold, convert_to_binary = threshold_options("Otsu", do_3d=False)
+    assert auto_threshold == ""
+    assert convert_to_binary == "method=Otsu background=Dark black"