Remove unnecessary function, its use, import and prints

Roi enlargement is not needed when using Cellpose for fiber detection

Remove unnecessary function, its use, import and prints
d4b365d8 · Kai Schleicher · e4613605 · d4b365d8
Commit d4b365d8 authored 2 weeks ago by Kai Schleicher
--- a/1_identify_fibers.py
+++ b/1_identify_fibers.py
@@ -12,7 +12,6 @@
 # @ Integer (label="Min perimeter [um]", value=5) minPer
 # @ Integer (label="Max perimeter [um]", value=300) maxPer
 # @ String (visibility=MESSAGE, value="<html><b> Expand ROIS to match fibers </b></html>") msg3
-# @ Double (label="ROI expansion [microns]", value=1) enlarge_radius
 # @ String (visibility=MESSAGE, value="<html><b> channel positions in the hyperstack </b></html>") msg5
 # @ Integer (label="Membrane staining channel number", style="slider", min=1, max=5, value=1) membrane_channel
 # @ Integer (label="Fiber staining (MHC) channel number (0=skip)", style="slider", min=0, max=5, value=3) fiber_channel
@@ -63,7 +62,7 @@ from fiji.plugin.trackmate.tracking.jaqaman import SparseLAPTrackerFactory
 from ij import IJ
 from ij import WindowManager as wm
 from ij.measure import ResultsTable
-from ij.plugin import Duplicator, ImageCalculator, RoiEnlarger
+from ij.plugin import Duplicator, ImageCalculator
 from imcflibs import pathtools
 from imcflibs.imagej import bioformats as bf
 from imcflibs.imagej import misc
@@ -490,26 +489,6 @@ def save_selected_rois(rm, selected_rois, target):
    rm.runCommand("Deselect")


-def enlarge_all_rois(amount_in_um, rm, pixel_size_in_um):
-    """Enlarges all ROIs in the RoiManager by x scaled units.
-
-    Parameters
-    ----------
-    amount_in_um : float
-        the value by which to enlarge in scaled units, e.g 3.5
-    rm : RoiManager
-        a reference of the IJ-RoiManager
-    pixel_size_in_um : float
-        the pixel size, e.g. 0.65 px/um
-    """
-    amount_px = amount_in_um / pixel_size_in_um
-    all_rois = rm.getRoisAsArray()
-    rm.reset()
-    for roi in all_rois:
-        enlarged_roi = RoiEnlarger.enlarge(roi, amount_px)
-        rm.addRoi(enlarged_roi)
-
-
 def select_positive_fibers(imp, channel, rm, min_intensity):
    """Select ROIs in ROIManager based on intensity in specific channel.

@@ -735,7 +714,6 @@ if __name__ == "__main__":
                IJ.log("area = " + str(minAr) + "-" + str(maxAr))
                IJ.log("perimeter = " + str(minPer) + "-" + str(maxPer))
                IJ.log("circularity = " + str(minCir) + "-" + str(maxCir))
-                IJ.log("ROI expansion [microns] = " + str(enlarge_radius))
                IJ.log("Membrane channel = " + str(membrane_channel))
                IJ.log("MHC positive fiber channel = " + str(fiber_channel))
                # IJ.log("sub-tiling = " + str(tiling_factor))
@@ -793,8 +771,6 @@ if __name__ == "__main__":
            misc.timed_log("Getting the ROIs")
            command.run(Labels2Rois, True, "rm", rm, "imp", imp_result).get()

-            misc.timed_log("Enlarging and renumbering the ROIs")
-            enlarge_all_rois(enlarge_radius, rm, raw_image_calibration.pixelWidth)
            renumber_rois(rm)

            misc.timed_log("Saving the ROIs")