Fix issue #96

Author: pradal

example/tutorials/1.import_and_read_MTG.ipynb

@@ -25,7 +25,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -44,7 +44,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -60,7 +60,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -88,19 +88,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "MTG : nb_vertices=158, nb_scales=4\n"
+     "ename": "KeyError",
+     "evalue": "'Breading_value'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[8], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m g \u001b[38;5;241m=\u001b[39m \u001b[43mimport_mtgfile\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfilename\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mBreading_value\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28mprint\u001b[39m(g)\n",
+      "File \u001b[0;32m~/devlp/git/strawberry/src/openalea/strawberry/import_mtgfile.py:41\u001b[0m, in \u001b[0;36mimport_mtgfile\u001b[0;34m(filename)\u001b[0m\n\u001b[1;32m     39\u001b[0m mtgfile \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mdict\u001b[39m((k,f) \u001b[38;5;28;01mfor\u001b[39;00m k,f \u001b[38;5;129;01min\u001b[39;00m mtg_path\u001b[38;5;241m.\u001b[39mitems() \u001b[38;5;28;01mif\u001b[39;00m k \u001b[38;5;129;01min\u001b[39;00m filenames)\n\u001b[1;32m     40\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(filenames) \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[0;32m---> 41\u001b[0m     g \u001b[38;5;241m=\u001b[39m MTG(\u001b[43mmtgfile\u001b[49m\u001b[43m[\u001b[49m\u001b[43mfilenames\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m]\u001b[49m)\n\u001b[1;32m     42\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m g\n\u001b[1;32m     43\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
+      "\u001b[0;31mKeyError\u001b[0m: 'Breading_value'"
      ]
     }
    ],
    "source": [
-    "g = import_mtgfile(filename= [\"Breadding_value\"])\n",
+    "g = import_mtgfile(filename= [\"Breading_value\"])\n",
     "print(g)\n"
    ]
   },
@@ -242,7 +247,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -256,7 +261,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.16"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

src/openalea/strawberry/import_mtgfile.py

@@ -100,13 +100,22 @@ def topology(df, first_property):
     string=[]
 
     for row in row_index:
+        empty = True
         for column in column_index:
             if array[row,column]!=-1:
+                empty = False
                 break
+        if empty: 
+            print("Error : Empty lines are forbidden")
+            continue
         if column == column_start:
             string.append(array[row,column])
         elif column < column_start:
-            string.extend([']',array[row,column]])
+            if column_start-column >1:
+                print('ERROR : ',column_start-column, ' LINE: ',row+2)
+                print(array[row-1,:])
+            nb = column_start-column
+            string.extend([']'*nb,array[row,column]])
         else:
             string.extend(['[',array[row,column]])
 
@@ -138,7 +147,9 @@ def test_string_convertion(string):
     if test_string_convertion(string)==0:
         return string
     else:
-        print("Error in convertion dataframe to string")
+        print("Error in convertion dataframe to string:")
+        print(string)
+        return string
 
 
 def add_properties(g, df, first_property):
@@ -188,9 +199,10 @@ def add_axis_scale(g):
             p_cpx = g.complex(pid)
 
             g.add_child(p_cpx, cpx, label="A", edge_type="+")
-            
-    g.reindex()
-    return g
+
+    new_g = g.reindex(copy=True)
+    
+    return new_g
 
 def strawberry_reader_csv(file, first_property='experimental_name',symbole_at_scale = dict(P=1,T=2, F=3, f=3, b=3, HT=3, bt=3, ht=3,s=3)):
     ''' Main function to import MTG from csv file
@@ -212,6 +224,7 @@ def strawberry_reader_csv(file, first_property='experimental_name',symbole_at_sc
     mtgs = list()
 
     for sheet in sheets:
+        print(f"{sheet}")
         df = read_file(file=file, sheet_name=sheet)  
 
         string= topology(df,first_property=first_property)
@@ -228,7 +241,15 @@ def strawberry_reader_csv(file, first_property='experimental_name',symbole_at_sc
 
         g= add_properties(g, df,first_property=first_property)
         g.property("Stade")
-        g= add_axis_scale(g)
+        try:
+            g= add_axis_scale(g)
+        except Exception as e:
+            print("#"*80)
+            print(f"{sheet} in ERROR")
+            print(g)
+            g.display()
+            raise(e)
+
         g.properties()["order"] = algo.orders(g)
         mtgs.append(g)