more work related to graffy/lipase#3

- the user can now use radial profile image processing through a new plugin (Radial Profile)
- improved the computation of the radial profile : the profile is now normalised (no longer bigger weights for big circles)

src/ij-plugins/Ipr/Lipase/Radial_Profile.py

@@ -0,0 +1,41 @@
+#@ ImagePlus (label="the input image") INPUT_IMAGE
+#@ Float (label="maximal radius", value=10.0, min=0.0, max=100.0, style="slider") MAX_RADIUS
+
+#@output ImagePlus RADIAL_PROFILE
+"""This script is supposed to be launched from fiji's jython interpreter
+
+This imagej plugin computes the radial profile of each pixel of the input image. The resulting profiles are stored in a single hyperstack, where the profile data are stored along the channel axis
+"""
+
+# # note: fiji's jython doesn't support encoding keyword
+
+import sys
+print('python version %s' % sys.version)  # prints python version
+
+from lipase.settings import UserSettings
+
+from lipase.imageengine import IImageEngine, PixelType
+from lipase.imagej.ijimageengine import IJImageEngine
+from lipase.circsymdetector import CircularSymmetryDetector
+
+import ij.gui  # pylint: disable=import-error
+from jarray import zeros, array  # pylint: disable=import-error
+
+def run_script():
+    global INPUT_IMAGE  # pylint:disable=global-variable-not-assigned
+    global MAX_RADIUS  # pylint:disable=global-variable-not-assigned
+    global RADIAL_PROFILE  # pylint:disable=global-variable-not-assigned
+
+    IImageEngine.set_instance(IJImageEngine())
+
+    src_image = IImageEngine.get_instance().create_image(width=1, height=1, pixel_type=PixelType.U8)
+    src_image.ij_image = INPUT_IMAGE  # pylint: disable=undefined-variable
+
+    detector = CircularSymmetryDetector(max_radius=MAX_RADIUS)  # pylint: disable=undefined-variable
+    radial_profiles = detector.compute_radial_profiles(src_image)
+
+    RADIAL_PROFILE = radial_profiles.hyperstack
+
+
+# note : when launched from fiji, __name__ doesn't have the value "__main__", as when launched from python
+run_script()

src/lipase/circsymdetector.py

@@ -41,7 +41,7 @@ def create_circle_image(image_size, circle_radius, circle_pos, circle_thickness,
             dx = x - circle_pos_x
             dy = y - circle_pos_y
             r_square = (dx * dx + dy * dy)
-            if r_min_square < r_square < r_max_square:
+            if r_min_square - 0.001 <= r_square < r_max_square:
                 pixel_value = circle_value
             else:
                 pixel_value = background_value
@@ -86,11 +86,15 @@ class CircularSymmetryProjectorBase(IProjectorBase):
         else:
             if oversampling_is_handled:
                 circle_image = oversampled_circle.resample(width=image_size, height=image_size)
-        # mean_value = circle_image.get_mean_value()
-        # num_pixels = image_size * image_size
-        # sum_of_pixel_values = mean_value * num_pixels
+        mean_value = circle_image.get_mean_value()
+        assert mean_value > 0.0, "unexpected mean value of this circle image : this circle might be empty, or worse, have negative values, which doesn't make sense"
+        print(type(mean_value))
+        num_pixels = image_size * image_size
+        sum_of_pixel_values = mean_value * num_pixels
         # we want each circle to have a total weight of 1.0, regardless their radius
-        # circle_image.scale_values(1.0/sum_of_pixel_values)
+        circle_image.scale_values(1.0/sum_of_pixel_values)
+        
+
         
         anchor_point = {'x': int(circle_pos['x']), 'y': int(circle_pos['y'])}
         return circle_image, anchor_point
@@ -119,5 +123,5 @@ class CircularSymmetryDetector:
             print(type(center_of_filter))
             projection = ie.filter2D(src_image, dst_type=PixelType.F32, kernel=projector, anchor=(center_of_filter['x'], center_of_filter['y']))
             ie.debugger.on_image(projection, 'projection_%d' % (projector_index))
-            radial_profile_image.set_image(self, projection, frame_index=0, slice_index=0, channel_index=projector_index)
+            radial_profile_image.set_image(projection, frame_index=0, slice_index=0, channel_index=projector_index)
         return radial_profile_image

src/lipase/imagej/ijimageengine.py

@@ -108,7 +108,8 @@ class IJImage(IImage):
         return image_stats.mean
 
     def scale_values(self, scale):
-        raise NotImplementedError()
+        processor = self.ij_image.getProcessor()
+        processor.multiply(scale)
 
 
 class IJHyperStack(IHyperStack):