Merge branch 'code-sebastien-20230418' into devel

Author: ehrenfeu

src/imcflibs/imagej/labelimage.py

@@ -20,7 +20,7 @@ def label_image_to_roi_list(label_image, low_thresh=None):
 
     Returns
     -------
-    roi_list : list(roi)  FIXME: what's the exact "roi" type?
+    roi_list : list(ij.gui.Roi)
         List of all the ROIs converted from the label image
     """
 

src/imcflibs/imagej/misc.py

@@ -4,9 +4,8 @@
 import time
 
 from ij import IJ  # pylint: disable-msg=import-error
-from ij.measure import ResultsTable  # pylint: disable-msg=import-error
-from ij.plugin.frame import RoiManager  # pylint: disable-msg=import-error
 
+from . import prefs
 from ..log import LOG as log
 
 
@@ -198,30 +197,24 @@ def get_free_memory():
     return free_memory
 
 
-def setup_clean_ij_environment(rm=None, rt=None):
+def setup_clean_ij_environment(rm=None, rt=None):  # pylint: disable-msg=unused-argument
     """Set up a clean and defined ImageJ environment.
 
+    Clean active results table, roi manager and log, close any open image.
+
+    "Fresh Start" is described here: https://imagej.nih.gov/ij/notes.html following this suggestion: https://forum.image.sc/t/fresh-start-macro-command-in-imagej-fiji/43102
+
     Parameters
     ----------
     rm : RoiManager, optional
-        A reference to an IJ-RoiManager instance.
+        Will be ignored (kept for keeping API compatibility).
     rt : ResultsTable, optional
-        A reference to an IJ-ResultsTable instance.
+        Will be ignored (kept for keeping API compatibility).
     """
-    # FIXME: use function(s) from the "roimanager" module!
-    if not rm:
-        rm = RoiManager.getInstance()
-        if not rm:
-            rm = RoiManager()
-
-    if not rt:
-        rt = ResultsTable.getInstance()
-        if not rt:
-            rt = ResultsTable()
-
-    rm.runCommand("reset")
-    rt.reset()
-    IJ.log(r"\\Clear")
-
-    # FIXME: integrate commands from method below
-    # fix_ij_options()
+
+    IJ.run("Fresh Start", "")
+    IJ.log("\\Clear")
+
+    prefs.fix_ij_options()
+
+    return

src/imcflibs/imagej/prefs.py

@@ -1,6 +1,6 @@
 """Functions to work with ImageJ preferences."""
 
-from ij import Prefs  # pylint: disable-msg=E0401
+from ij import Prefs, IJ  # pylint: disable-msg=E0401
 
 
 def debug_mode():
@@ -18,3 +18,21 @@ def debug_mode():
     """
     debug = Prefs.get("imcf.debugging", "false")
     return debug == "true"
+
+
+def fix_ij_options():
+    """Wrapper to setup ImageJ default options."""
+
+    # disable inverting LUT
+    IJ.run("Appearance...", " menu=0 16-bit=Automatic")
+    # set foreground color to be white, background black
+    IJ.run("Colors...", "foreground=white background=black selection=red")
+    # black BG for binary images and pad edges when eroding
+    IJ.run("Options...", "black pad")
+    # set saving format to .txt files
+    IJ.run("Input/Output...", "file=.txt save_column save_row")
+    # ============= DON'T MOVE UPWARDS =============
+    # set "Black Background" in "Binary Options"
+    IJ.run("Options...", "black")
+    # scale when converting = checked
+    IJ.run("Conversions...", "scale")