Fixes for profile script

demos/T-Junction/ini_KO_240_050_240.xml

@@ -5,7 +5,7 @@
 	<!-- trajectories file and format -->
 	<!-- either a file name or a path location. In the latter case all files in the directory will be used-->
 	<trajectories format="txt" unit="m">
-		<file name="traj_KO_240_050_240_x.txt" />
+		<file name="traj_KO_240_050_240.txt" />
 		<path location="./" />  
 	</trajectories>
 	<!-- give relative path based on the location inifile or give the absolute path- -->
@@ -37,14 +37,14 @@
 		</area_L>
 	</measurement_areas>
 
-<!--	<velocity>
+	<velocity>
 		<use_x_component>true</use_x_component>
 		<use_y_component>true</use_y_component>
         		<!-- The time interval that used to calculate instantaneous velocity 
-			of ped i [fr] here v_i = (X(t+frame_step/2) - X(t+frame_step/2))/frame_step. X is location. 
+			of ped i [fr] here v_i = (X(t+frame_step/2) - X(t+frame_step/2))/frame_step. X is location. -->
 		<frame_step>10</frame_step>
 	</velocity>
--->   
+
     <velocity frame_step="10" set_movement_direction="None" ignore_backward_movement="false"/>
     <!-- frame_step is the time interval that used to calculate instantaneous velocity 
 	of ped i [fr] here v_i = (X(t+frame_step/2) - X(t+frame_step/2))/frame_step. X is location. -->
@@ -62,19 +62,18 @@
 	</method_B>
 
 	<!-- Method C (Zhang2011a) Classical density and Vel -->
-	<method_C enabled="true">
+	<method_C enabled="false">
 		<measurement_area id="1" plot_time_series="true"/>
         <measurement_area id="2" plot_time_series="true"/>
 	</method_C>
 	
 	<!-- Method D (Zhang2011a) Voronoi density and Vel -->
 	<method_D enabled="true"> 
-        <measurement_area id="1" start_frame="None" stop_frame="None" get_individual_FD="false" plot_time_series="true"/> 
-        <measurement_area id="2" start_frame="500" stop_frame="800" get_individual_FD="false" plot_time_series="true"/> 
+        <measurement_area id="1" start_frame="500" stop_frame="800" get_individual_FD="false" plot_time_series="true"/> 
 		<one_dimensional enabled="false"/>
         <cut_by_circle enabled="false" radius="1.0" edges="10"/>
         <output_voronoi_cells enabled="false" plot_graphs="false"/>
-        <profiles enabled="false" grid_size_x="0.20" grid_size_y="0.20"/> 
+        <profiles enabled="true" grid_size_x="0.20" grid_size_y="0.20"/> 
     </method_D> 
 </JPSreport>
 

scripts/_Plot_profiles.py

@@ -22,10 +22,10 @@ def get_parser_args():
                                                                              'steady state')
     parser.add_argument("-e", "--endsteady", type=int, required=True, help='the frame for the ending of '
                                                                            'steady state')
-    parser.add_argument("-x1", "--geominx", type=float, required=True, help='the minmum x of the geometry')
-    parser.add_argument("-x2", "--geomaxx", type=float, required=True, help='the maxmum x of the geometry')
-    parser.add_argument("-y1", "--geominy", type=float, required=True, help='the minmum y of the geometry')
-    parser.add_argument("-y2", "--geomaxy", type=float, required=True, help='the maxmum y of the geometry')
+    parser.add_argument("-x1", "--geominx", type=float, required=True, help='the minimum x of the geometry')
+    parser.add_argument("-x2", "--geomaxx", type=float, required=True, help='the maximum x of the geometry')
+    parser.add_argument("-y1", "--geominy", type=float, required=True, help='the minimum y of the geometry')
+    parser.add_argument("-y2", "--geomaxy", type=float, required=True, help='the maximum y of the geometry')
     arguments = parser.parse_args()
     return arguments
 
@@ -66,11 +66,14 @@ if __name__ == '__main__':
     ax1 = fig.add_subplot(111, aspect='1')
     plt.rc("font", size=40)
     for j in range(beginsteady, endsteady):
-        density_file = os.path.join(
-            pathfile, "density", "Prf_d_%s
-_id_1_%.5d.dat" % (nametraj, j))
-        print("loading: %s" % density_file)
-        density += np.loadtxt(density_file)
+        density_file = os.path.join(pathfile, "density", "Prf_d_%s_id_1_%.5d.dat" %(nametraj, j))
+        if os.path.exists(density_file):
+            print("loading: %s" % density_file)
+            density += np.loadtxt(density_file)
+            
+        else:
+            print("WARNING: file not found %s"%density_file)
+        
 
     density = density / (endsteady - beginsteady)
 
@@ -97,9 +100,11 @@ _id_1_%.5d.dat" % (nametraj, j))
     for j in range(beginsteady, endsteady):
         velocity_file = os.path.join(
             pathfile, "velocity", "Prf_v_%s_id_1_%.5d.dat" % (nametraj, j))
-        print("loading: %s" % velocity_file)
-        velocity += np.loadtxt(velocity_file)
-
+        if os.path.exists(velocity_file):
+                print("loading: %s" % velocity_file)
+                velocity += np.loadtxt(velocity_file)
+        else:
+            print("WARNING: file not found %s"%velocity_file)
     velocity = velocity / (endsteady - beginsteady)
     im = plt.imshow(velocity,
                     cmap=cm.jet,