choose between local/appose mode for each case

Author: gletort

src/fish_feats/MainImage.py

@@ -362,7 +362,7 @@ def separate_junctions_nuclei( self, wth_radxy=4, wth_radz=1, rmoutlier_radxy=5,
 
     def separate_with_sepanet( self, model_dir ):
         bothimage = np.copy(self.image[self.nucchan,])
-        if ut.full_fishfeats:
+        if ut.has_dependency( "tensorflow" ):
             from fish_feats.Separe import sepanet_local
             self.junstain, self.nucstain = sepanet_local( bothimage, model_dir )
         else:

src/fish_feats/SegmentObj.py

@@ -136,7 +136,7 @@ def run_epyseg_onimage(img, filedir, filename, verbose=True):
 
     binimg = None
     tmpdir_path = None
-    appose = not ut.full_fishfeats()
+    appose = not ut.has_dependency( "epyseg" )
     try:
         with tempfile.TemporaryDirectory() as tmpdir:
             print("tmp dir "+str(tmpdir))
@@ -458,7 +458,7 @@ def getNuclei_stardist2DAsso3D(nucimg, scaleXY, proba=0.55, overlap=0.1, assoMod
     """ Segment nuclei with Stardist2D and reconstruct in 3D - return the nuclei list """
 
     ## segment 2D
-    appose = not ut.full_fishfeats()
+    appose = not ut.has_dependency( "stardist" )
     if appose:
         labnuc = stardist2D_appose(nucimg, prob=proba, over=overlap, progress_bar=progress_bar)
     else:

src/fish_feats/Utils.py

@@ -805,13 +805,20 @@ def version_napari_above( compare_version ):
     """ Get the current version of napari """
     return Version(napari.__version__) > Version(compare_version)
 
-def full_fishfeats():
+def has_dependency( depname ):
     """ Check if installation was done with full mode or appose mode """
     try: 
-        import stardist 
-        return False
+        if depname == "stardist":
+            import stardist 
+            return True
+        elif depname == "epyseg":
+            import epyseg
+            return True
+        elif depname == "tensorflow":
+            import tensorflow as tf
+            return True
     except:
-        return True
+        return False
 
 def add_point_layer( viewer, pts, colors, layer_name, mig, size=7, pts_properties=None ):
     """ Add a points layer to the viewer """