added some new regression tests for epsmap and blobby surf validation

tests/6xm4_blobby/6xm4_blobby_conf.prm

+###############################################################################
+###################### NanoShaper 0.3.1 Configuration file  ###################
+###############################################################################
+
+Compute_Vertex_Normals = true
+Save_Mesh_MSMS_Format = true
+Load_Balancing = true
+Print_Available_Surfaces = false
+
+Example_Surface_Parameter = 2.0
+
+# NOTE
+# for big molecules consider reducing to 1.5 for limiting memory usage.
+# if still memory usage is too high, remove accurate triangulation 
+# and enable status map
+
+################################ Grid params ##################################
+
+# Grid scale 
+Grid_scale = 1.0
+
+# Percentage that the surface occupies with respect to the total grid volume 
+# default value is 90.0; in the case of very small molecules (e.g. fullerene) keep more margin 
+# (e.g. lower the value to 50%)
+Grid_perfil = 90.0 
+
+# Input atoms xyzr file name
+XYZR_FileName = 6xm4.xyzr
+
+############################## Internal maps ##################################
+
+# Enable/Disable build of epsilon (dielectric) map
+Build_epsilon_maps  = false
+
+# Enable/Disable build of map for cavity detection and for a non analytical
+# triangulation
+Build_status_map = true
+
+########################## Surface Type params ################################
+
+# Possible values: skin,blobby,mesh,ses,example
+Surface = blobby
+
+# Apply final surface smoothing
+Smooth_Mesh = false
+
+# Number of total threads
+Number_thread = 16 
+
+# Skin surface parameter [0.05,0.95]
+# the extrema are possibly not numerically stable,
+# the suggested range is [0.15,0.95]
+# default value is 0.45
+Skin_Surface_Parameter = 0.45
+
+# Blobbyness value for the blobby surface [-0.5,-5.0]
+# default value is -2.5
+Blobbyness = -2.5 
+
+# Name of the input surface file used if mesh Surface is enabled or msms.
+# In case of msms remove any extension, .face and .vert file will be 
+# automatically loaded.
+# In case of mesh, .off and .ply files are supported
+Surface_File_Name = triangulatedSurf.vert
+
+######################## Surface Processing params ############################
+# Enable or disable cavity detection together with the volume conditional
+# filling of voids and cavities
+Cavity_Detection_Filling = false
+
+# It is the value of the minimal volume of a cavity to get filled if 
+# cavity detection is enabled. 
+# The default value is an approximation of the volume of the water molecule 
+# default value is 11.4, this is the approximate volume of a water molecule 
+# in Angstrom
+Conditional_Volume_Filling_Value = 11.4
+
+# If this flag is true, cavities where a sphere of Probe_Radius cannot fit, 
+# are removed.
+# Use this feature when cavity detection is enabled to filter out bad shaped 
+# cavities whose
+# volume is higher than Conditional_Volume_Filling_Value.
+Keep_Water_Shaped_Cavities = false
+
+# The radius of the sphere that represents a water molecule in Angstrom
+# default value is 1.4 Angstrom
+Probe_Radius = 1.4
+
+# Enable accurate triangulation: if accurate triangulation is enable all points 
+# are sampled from the original surface. If disabled the points are not 
+# analytically sampled and an high memory saving can be obtained
+# together with a 3x speed-up on ray casting if both epsmap is disabled
+# MC phase will be slower because vertices are calculated on the fly
+Accurate_Triangulation = true
+
+# Perform triangulation using a single ray-casting process. Vertex data is 
+# inferred.
+Triangulation = true
+
+# Check duplicated vertices when reading
+Check_duplicated_vertices = false
+
+# If true save the status map. Enable this for cavity detection and 
+# visualization of the coloured FD grid
+Save_Status_map = false
+
+# Save Skin/SES in a PovRay file for ray-tracing. 
+# This is a purely graphics representation because the surface is not in
+# a left handed system as it should in Pov-Ray
+Save_PovRay = false
+
+####################### Acceleration Data Structures ##########################
+
+# Mesh Projection(3D)/Ray Casting (3D) acceleration grid
+# Increase *_size to increase performance and memory usage.
+# Increase *_cell if requested by NanoShaper
+
+# default 100
+Max_mesh_auxiliary_grid_size = 100
+# default 250
+Max_mesh_patches_per_auxiliary_grid_cell = 250;
+# default 100
+Max_mesh_auxiliary_grid_2d_size = 100
+# default 250
+Max_mesh_patches_per_auxiliary_grid_2d_cell = 250 
+
+# SES Projection(3D)/Ray Casting (3D) acceleration grid
+# default 100
+Max_ses_patches_auxiliary_grid_size = 100
+# default 400
+Max_ses_patches_per_auxiliary_grid_cell = 400
+# defualt 40
+Max_ses_patches_auxiliary_grid_2d_size = 40
+# default 400
+Max_ses_patches_per_auxiliary_grid_2d_cell = 400
+
+# Skin Projection(3D)/Ray Casting (3D) acceleration grid
+# default 100
+Max_skin_patches_auxiliary_grid_size = 100
+# default 400
+Max_skin_patches_per_auxiliary_grid_cell = 400
+# default 50
+Max_skin_patches_auxiliary_grid_2d_size = 50
+# default 400
+Max_skin_patches_per_auxiliary_grid_2d_cell = 600
+
+###############################################################################

tests/6xm4_skin/6xm4_skin_conf.prm

@@ -26,13 +26,11 @@ Grid_perfil = 90.0
 
 # Input atoms xyzr file name
 XYZR_FileName = 6xm4.xyzr
-#XYZR_FileName = 1vsz.xyzr 
-#XYZR_FileName = 1crn.xyzr
 
 ############################## Internal maps ##################################
 
 # Enable/Disable build of epsilon (dielectric) map
-Build_epsilon_maps  = false
+Build_epsilon_maps  = true
 
 # Enable/Disable build of map for cavity detection and for a non analytical
 # triangulation
@@ -104,7 +102,8 @@ Check_duplicated_vertices = false
 
 # If true save the status map. Enable this for cavity detection and 
 # visualization of the coloured FD grid
-Save_Status_map = false
+Save_Status_map = true
+Save_eps_maps = true
 
 # Save Skin/SES in a PovRay file for ray-tracing. 
 # This is a purely graphics representation because the surface is not in

tests/ns_test.py

@@ -6,6 +6,7 @@ import json
 import time
 import tarfile
 import shutil
+import filecmp
     
 
 class ns_test:
@@ -33,6 +34,7 @@ class ns_test:
         self.outmsg = ''
         self.shapemsg = ''
         self.valuemsg = ''
+        self.mapsmsg = ''
         self.execmsg = ''
         self.genmsg = ''
 
@@ -49,10 +51,19 @@ class ns_test:
         return True
 
     def is_area_file(self,p_filepath):
-        name, ext = os.path.splitext(p_filepath)
-        if ext != '.txt':
-            return False
-        return True
+        if 'Areas' in p_filepath:
+            return True
+        return False
+
+    def is_epsmap_file(self,p_filepath):
+        if 'epsmap' in p_filepath:
+            return True
+        return False
+
+    def is_status_file(self,p_filepath):
+        if 'status' in p_filepath:
+            return True
+        return False
 
     def read_vert(self,p_filepath):
         
@@ -135,6 +146,8 @@ class ns_test:
         compare the shapes and values between output and reference arrays
         .OFF values 
         Area values
+        .VERT values
+        MAPS
 
         :param p_file name of the file containing values 
         
@@ -193,6 +206,16 @@ class ns_test:
                         self.valuemsg = "{} {}".format(self.valuemsg, p_file)
                         self.failed = True
 
+            elif self.is_epsmap_file(p_file):
+                if not filecmp.cmp(ref_file_path,out_file_path,shallow=False):
+                    self.mapsmsg = "{} {}".format(self.mapsmsg, p_file)
+                    self.failed = True
+
+            elif self.is_status_file(p_file):
+                if not filecmp.cmp(ref_file_path,out_file_path,shallow=False):
+                    self.mapsmsg = "{} {}".format(self.mapsmsg, p_file)
+                    self.failed = True
+
             elif self.is_area_file(p_file):      
                 ref_areas = self.read_area(ref_file_path)
                 areas = self.read_area(out_file_path)
@@ -339,6 +362,9 @@ class ns_test:
             if self.valuemsg != '':
                 self.valuemsg = "Different values in files: {} ".format(self.valuemsg)  
                 print(self.valuemsg)
+            if self.mapsmsg != '':
+                self.mapsmsg = "Different maps in files: {} ".format(self.mapsmsg)  
+                print(self.mapsmsg)
             if self.genmsg != '':
                self.genmsg = "Generic Errors: {}".format(self.genmsg)
                print(self.genmsg)