change selem to footprint in skimage.morphology funcs

ihesp · Jul 12, 2023 · 544aec0 · 544aec0
1 parent bccbaff
commit 544aec0
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Showing 2 changed files with 46 additions and 8 deletions.
diff --git a/ipart/AR_detector.py b/ipart/AR_detector.py
@@ -763,7 +763,13 @@ def partPeaks(cropmask, cropidx, orislab, area, min_area, max_ph_ratio,
         ele=morphology.diamond(fill_radius//2)
 
         gap=cropmask-mask1
-        op=morphology.opening(mask1, selem=ele)
+
+        try:
+            op=morphology.opening(mask1, selem=ele)
+        except:
+            # version >= 0.19 changes to footprint
+            op=morphology.opening(mask1, footprint=ele)
+
         gap2=morphology.reconstruction(gap, mask1-op+gap)
         mask1=np.where(mask1-gap2<=0, 0, mask1)
         #gap2=morphology.dilation(gap, selem=ele)
@@ -1621,7 +1627,11 @@ def paddedClosing(mask, ele, pad, has_cv):
         if has_cv:
             padmask=cv.morphologyEx(padmask, cv.MORPH_CLOSE, ele)
         else:
-            padmask=morphology.closing(padmask, selem=ele)
+            try:
+                padmask=morphology.closing(padmask, selem=ele)
+            except:
+                # version >= 0.19 changes to footprint
+                padmask=morphology.closing(padmask, footprint=ele)
         # trim
         padmask=padmask[tuple([slice(pad,-pad), slice(pad,-pad)])]
         return padmask

diff --git a/ipart/thr.py b/ipart/thr.py
@@ -102,12 +102,20 @@ def THR(ivtNV, kernel, oroNV=None, high_terrain=600, verbose=True):
     if verbose:
         print('\n# <THR>: Computing erosion ...')
 
-    lm=morphology.erosion(ivt, selem=ele)
+    try:
+        lm=morphology.erosion(ivt, selem=ele)
+    except TypeError:
+        # version >= 0.19 changes to footprint
+        lm=morphology.erosion(ivt, footprint=ele)
 
     if verbose:
         print('\n# <THR>: Computing reconstruction ...')
 
-    ivtrec=morphology.reconstruction(lm, ivt, method='dilation', selem=rec_ele)
+    try:
+        ivtrec=morphology.reconstruction(lm, ivt, method='dilation', selem=rec_ele)
+    except TypeError:
+        # version >= 0.19 changes to footprint
+        ivtrec=morphology.reconstruction(lm, ivt, method='dilation', footprint=rec_ele)
 
     # perform an extra reconstruction over land
     if oroNV is not None:
@@ -116,8 +124,14 @@ def THR(ivtNV, kernel, oroNV=None, high_terrain=600, verbose=True):
         oro_rs=oro_rs[None,...]
         oro_rs=np.repeat(oro_rs, len(ivt), axis=0)
 
-        ivtrec_oro=morphology.reconstruction(lm*oro_rs, ivt, method='dilation',
-                selem=rec_ele)
+        try:
+            ivtrec_oro=morphology.reconstruction(lm*oro_rs, ivt, method='dilation',
+                    selem=rec_ele)
+        except TypeError:
+        # version >= 0.19 changes to footprint
+            ivtrec_oro=morphology.reconstruction(lm*oro_rs, ivt, method='dilation',
+                    footprint=rec_ele)
+
         ivtano=np.ma.maximum(ivt-ivtrec, (ivt-ivtrec_oro)*oro_rs)
     else:
         ivtano=ivt-ivtrec
@@ -386,21 +400,35 @@ def THRCyclicLongitude(ivt, kernel, oro=None, high_terrain=600, verbose=True):
     if verbose:
         print('\n# <THR>: Computing erosion ...')
 
-    lm=morphology.erosion(ivt.data, selem=ele)
+    try:
+        lm=morphology.erosion(ivt.data, selem=ele)
+    except TypeError:
+        # version >= 0.19 changes to footprint
+        lm=morphology.erosion(ivt.data, footprint=ele)
 
     if verbose:
         print('\n# <THR>: Computing reconstruction ...')
 
-    ivtrec=recon.reconstruction(lm, ivt, method='dilation', selem=rec_ele)
+    try:
+        ivtrec=recon.reconstruction(lm, ivt, method='dilation', selem=rec_ele)
+    except TypeError:
+        # version >= 0.19 changes to footprint
+        ivtrec=recon.reconstruction(lm, ivt, method='dilation', footprint=rec_ele)
 
     # perform an extra reconstruction over land
     if oro is not None:
         oro_rs=MV.where(oro>=high_terrain, 1, 0)
         oro_rs=funcs.addExtraAxis(oro_rs,axis=0)
         oro_rs=np.repeat(oro_rs, len(ivt), axis=0)
 
+    try:
         ivtrec_oro=recon.reconstruction(lm*oro_rs, ivt, method='dilation',
                 selem=rec_ele)
+    except TypeError:
+        # version >= 0.19 changes to footprint
+        ivtrec_oro=recon.reconstruction(lm*oro_rs, ivt, method='dilation',
+                footprint=rec_ele)
+
         ivtano=MV.maximum(ivt-ivtrec, (ivt-ivtrec_oro)*oro_rs)
     else:
         ivtano=ivt-ivtrec