Python 3 compatibility

bemio/__init__.py

@@ -1 +1,2 @@
-from __version__ import base, full
+from __future__ import absolute_import
+from .__version__ import base, full

bemio/data_structures/bem.py

@@ -11,8 +11,8 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-from __future__ import division
 
+from __future__ import division
 import numpy as np
 
 import os
@@ -266,9 +266,9 @@ def calc_irf_excitation(self, t_end=100.0, n_t=1001, n_w=1001, w_min=None, w_max
         count = 1
         for t_ind, t in enumerate(self.ex.irf.t):
 
-          for i in xrange(self.ex.mag.shape[0]):
+          for i in range(self.ex.mag.shape[0]):
 
-            for j in xrange(self.ex.mag.shape[1]):
+            for j in range(self.ex.mag.shape[1]):
               tmp = ex_re_interp[i, j, :] * np.cos(self.ex.irf.w * t) - ex_im_interp[i, j, :] * np.sin(self.ex.irf.w * t)
               tmp *= 1. / np.pi
               self.ex.irf.f[i, j, t_ind] = np.trapz(y=tmp, x=self.ex.irf.w)
@@ -353,9 +353,9 @@ def calc_irf_radiation(self, t_end=100., n_t=1001, n_w=1001, w_min=None, w_max=N
         count = 1
         for t_ind, t in enumerate(self.rd.irf.t):
 
-            for i in xrange(self.rd.all.shape[0]):
+            for i in range(self.rd.all.shape[0]):
 
-                for j in xrange(self.rd.all.shape[1]):
+                for j in range(self.rd.all.shape[1]):
               # Radiation damping calculation method
                     tmpL = 2. / np.pi * rd_interp[i, j, :] * np.sin(self.rd.irf.w * t)
                     tmpK = 2. / np.pi * rd_interp[i, j, :] * np.cos(self.rd.irf.w * t)
@@ -426,9 +426,9 @@ def calc_ss_radiation(self, max_order=10, r2_thresh=0.95):
 
         pbar = ProgressBar(widgets=['Radiation damping state space realization for ' + self.name + ':', Percentage(), Bar()], maxval=self.am.inf.shape[0] * self.am.inf.shape[1]).start()
         count = 0
-        for i in xrange(self.am.inf.shape[0]):
+        for i in range(self.am.inf.shape[0]):
 
-          for j in xrange(self.am.inf.shape[1]):
+          for j in range(self.am.inf.shape[1]):
 
             r2bt = np.linalg.norm(
                 self.rd.irf.K[i, j, :] - self.rd.irf.K.mean(axis=2)[i, j])
@@ -472,7 +472,7 @@ def calc_ss_radiation(self, max_order=10, r2_thresh=0.95):
                 # D - T/2C (2/T(I + A)^{-1})B  = D - C(I + A)^{-1})B
                 dc = d + CoeC * np.dot(np.dot(c, iidd), b)
 
-                for jj in xrange(self.rd.irf.t.size):
+                for jj in range(self.rd.irf.t.size):
 
                   # Calculate impulse response function from state space
                   # approximation
@@ -549,11 +549,11 @@ def scale(self, scale=None):
             self.scale = scale
 
         if self.scale is True and self.scaled is False:
-          print '\tScaling hydro coefficients for body ' + self.name + ' by rho, g, and w...'
+          print('\tScaling hydro coefficients for body ' + self.name + ' by rho, g, and w...')
           try:
               self.k *= self.rho * self.g
           except:
-              print '\t\tSpring stiffness not scaled'
+              print('\t\tSpring stiffness not scaled')
 
           self.am.all *= self.rho
           self.am.inf *= self.rho
@@ -575,18 +575,18 @@ def scale(self, scale=None):
               self.ex.fk.im *= self.rho * self.g
 
 
-          for j in xrange(self.rd.all.shape[2]):
+          for j in range(self.rd.all.shape[2]):
 
             self.rd.all[:, :, j] = self.rd.all[:, :, j] * self.rho * self.w[j]
 
           self.scaled = True
 
         elif self.scale is False and self.scaled is True:
-          print '\tUn-scaling hydro coefficients for body ' + self.name + ' by rho, g, and w...'
+          print('\tUn-scaling hydro coefficients for body ' + self.name + ' by rho, g, and w...')
           try:
               self.k /= (self.rho * self.g)
           except:
-              print '\t\tSpring stiffness not un-scaled'
+              print('\t\tSpring stiffness not un-scaled')
           self.am.all /= self.rho
           self.am.inf /= self.rho
           if hasattr(self.am,'zero') is True:
@@ -606,7 +606,7 @@ def scale(self, scale=None):
               self.ex.fk.re /= (self.rho * self.g)
               self.ex.fk.im /= (self.rho * self.g)
 
-          for j in xrange(self.rd.all.shape[2]):
+          for j in range(self.rd.all.shape[2]):
 
             self.rd.all[:, :, j] = self.rd.all[:, :, j] / (self.rho * self.w[j])
 
@@ -630,9 +630,9 @@ def _interpolate_for_irf(w_orig, w_interp, mat_in):
 
     w_tmp = w_orig
 
-  for i in xrange(mat_in.shape[0]):
+  for i in range(mat_in.shape[0]):
 
-    for j in xrange(mat_in.shape[1]):
+    for j in range(mat_in.shape[1]):
 
       if flip is True:
 

bemio/data_structures/wave_excitation.py

@@ -74,7 +74,7 @@ def _excitation_convolution(self):
         irf_interp = interpolate.interp1d(x=self.irf.t, y=self.irf.f, bounds_error=False, fill_value=0.)
 
         # Interpolate the IRF to the dt as the wave elevation data
-        irf = irf_interp(np.linspace(self.irf.t.min(),self.irf.t.max(),(self.irf.t.max()-self.irf.t.min())/self.wave_elevation.dt+1))
+        irf = irf_interp(np.arange(self.irf.t.min(),self.irf.t.max(),(self.irf.t.max()-self.irf.t.min())/self.wave_elevation.dt+1))
 
         # Assume that the IRF dt is used unless specified by the user
         # if self.excitation_force.dt is None:

bemio/io/aqwa.py

@@ -12,8 +12,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import print_function
 import numpy as np
-
 from bemio.data_structures import bem
 
 from math import ceil
@@ -40,7 +40,7 @@ class AqwaOutput(object):
     '''
     def __init__(self, hydro_file, list_file, scale=False):
 
-        print '\nReading the AQWA results in the ' + hydro_file + ' file'
+        print('\nReading the AQWA results in the ' + hydro_file + ' file')
 
         self.files = bem.generate_file_names(hydro_file)
         self.scaled_at_read = scale
@@ -194,10 +194,10 @@ def _read(self,list_file):
                 bod_count += 1
 
 
-        for i in xrange(num_bodies):
+        for i in range(num_bodies):
 
 
-            print 'body' + str(i+1) + ':'
+            print('body' + str(i+1) + ':')
 
             self.body[i] = bem.HydrodynamicData()
             self.body[i].scaled = self.scaled
@@ -224,14 +224,14 @@ def _read(self,list_file):
             self.body[i].bem_raw_data = raw
 
             self.body[i].am.all = np.copy(added_mass[i+1])
-            print '   * Setting added mass at infinite frequency to added mass at omega = ' + str(frequencies[-1])
+            print('   * Setting added mass at infinite frequency to added mass at omega = ' + str(frequencies[-1]))
             self.body[i].am.inf = np.copy(added_mass[i+1][:,:,-1])
-            print '   * Setting added mass at zero frequency to added mass at omega = ' + str(frequencies[0])
+            print('   * Setting added mass at zero frequency to added mass at omega = ' + str(frequencies[0]))
             self.body[i].am.zero = np.copy(added_mass[i+1][:,:,0])
             self.body[i].rd.all = radiation_damping[i+1]
             self.body[i].ex.mag = excitation_magnitude[i+1]
             self.body[i].ex.phase = excitation_phase[i+1]
-            print '   * Calculating real and imaginary excitation  components.'
+            print('   * Calculating real and imaginary excitation  components.')
             self.body[i].ex.re = self.body[i].ex.mag * np.cos(self.body[i].ex.phase*np.pi/180.)
             self.body[i].ex.im = self.body[i].ex.mag * np.sin(self.body[i].ex.phase*np.pi/180.)
 

bemio/io/nemoh.py

@@ -11,6 +11,8 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+
+from __future__ import print_function
 from __future__ import division
 
 import os
@@ -60,7 +62,7 @@ def __init__(self, sim_dir='./', cal_file='Nemoh.cal', results_dir = 'Results',
         self.scaled = True
         self.dir = os.path.abspath(sim_dir)
 
-        print '\nReading NEMOH output in the ' + self.dir + ' directory'
+        print('\nReading NEMOH output in the ' + self.dir + ' directory')
 
         self.files = bem.generate_file_names(os.path.join(self.dir,cal_file))
         self.files['Nemoh']     = os.path.join(self.dir,cal_file)
@@ -75,7 +77,7 @@ def __init__(self, sim_dir='./', cal_file='Nemoh.cal', results_dir = 'Results',
         try:
             self.files['IRF'] = os.path.join(self.dir,results_dir,'IRF.tec')
         except:
-            print '\tNo IRF forces or infinite frequency added mass forces read because the ' + self.files['IRF'] + ' was not found'
+            print('\tNo IRF forces or infinite frequency added mass forces read because the ' + self.files['IRF'] + ' was not found')
 
         # Initialize data ovject
         self.body = {}
@@ -110,7 +112,7 @@ def _create_and_load_hydro_data_obj(self):
         '''
         Function to load hydrodynamic data into HydrodynamicData object
         '''
-        for i in xrange(self.cal.n_bods):
+        for i in range(self.cal.n_bods):
             self.body[i] = bem.HydrodynamicData()
             self.body[i].am.all = self.am[0+6*i:6+6*i,:]
             self.body[i].rd.all = self.rd[0+6*i:6+6*i,:]
@@ -168,7 +170,7 @@ def _read_cal(self):
 
         # Read wave directions
         temp = cal[-6]
-        self.cal.wave_dir_n = np.float(temp.split()[0])
+        self.cal.wave_dir_n = np.int32(temp.split()[0])
         self.cal.wave_dir_start = np.float(temp.split()[1])
         self.cal.wave_dir_end = np.float(temp.split()[2])
         self.cal.wave_dir = np.linspace(self.cal.wave_dir_start,self.cal.wave_dir_end,self.cal.wave_dir_n)
@@ -189,28 +191,28 @@ def _read_cal(self):
         self.cal.add_lines = {}
         self.cal.cg = {}
         line_count = 0
-        for i in xrange(self.cal.n_bods):
+        for i in range(self.cal.n_bods):
             name_with_path = cal[8+line_count].split()[0]
             self.cal.name[i] = os.path.splitext(os.path.basename(name_with_path))[0]
             self.cal.points_panels[i] = cal[9+line_count].split()[0:2]
             self.cal.n_dof[i] = int(cal[10+line_count].split()[0])
             self.cal.dof[i] = []
             self.cal.forces[i] = []
             self.cal.add_lines[i] = []
-            for j in xrange(self.cal.n_dof[i]):
+            for j in range(self.cal.n_dof[i]):
                 self.cal.dof[i].append(cal[11+line_count+j])
 
                 if int(self.cal.dof[i][-1].split()[0]) == 2:
                     self.cal.cg[i] = np.array(self.cal.dof[i][-1].split()[4:7],dtype=float)
 
             self.cal.n_forces[i] = int(cal[10+line_count+self.cal.n_dof[i]+1].split()[0])
 
-            for j in xrange(self.cal.n_forces[i]):
+            for j in range(self.cal.n_forces[i]):
                     self.cal.forces[i].append(cal[11+line_count+j+self.cal.n_dof[i]+1])
 
             self.cal.n_add_lines[i] = int(cal[10 + line_count + self.cal.n_dof[i] + self.cal.n_forces[i] + 2].split()[0])
 
-            for j in xrange(self.cal.n_add_lines[i]):
+            for j in range(self.cal.n_add_lines[i]):
                     self.cal.add_lines[i].append(cal[11+line_count+j+self.cal.n_dof[i]+self.cal.n_forces[i]+1])
 
             line_count += self.cal.n_dof[i] + self.cal.n_forces[i] + self.cal.n_add_lines[i] + 6
@@ -247,7 +249,7 @@ def read_kh(self, file, body_num):
 
         if self.body[body_num].scaled is False:
             self.body[body_num].k /= (self.body[body_num].rho * self.body[body_num].g)
-            print '\tSpring stiffness for body ' + self.body[body_num].name + ' scaled by read_kh method'
+            print('\tSpring stiffness for body ' + self.body[body_num].name + ' scaled by read_kh method')
 
     def read_hydrostatics(self, file, body_num):
         '''
@@ -326,7 +328,7 @@ def _read_tec(file, data_type):
 
 
     # Sort the zones from the .tec file
-    zones = proc.keys()
+    zones = list(proc)
     zones.sort()
 
     # Set the frequencies and calculate number of freqs
@@ -342,13 +344,13 @@ def _read_tec(file, data_type):
         b = []
 
     if data_type == 1:
-        for j in xrange(n_vars):
+        for j in range(n_vars):
             a[j,0,:] = proc[zones[-1]].field(1+j*2)
             b[j,0,:] = proc[zones[-1]].field(2+j*2)
 
     if data_type == 2:
         for i, zone in enumerate(zones):
-            for j in xrange(n_vars):
+            for j in range(n_vars):
                 a[i,j] = proc[zone].field(1+j*2)[0]
 
     return (a, b, w, raw)
@@ -379,7 +381,7 @@ def _read_radiation(file, ):
 
 
     # Sort the zones from the .tec file
-    zones = proc.keys()
+    zones = list(proc.keys())
     zones.sort()
 
     # Set the frequencies and calculate number of freqs
@@ -392,7 +394,7 @@ def _read_radiation(file, ):
 
     # Populate matrices
     for i, zone in enumerate(zones):
-        for j in xrange(n_vars):
+        for j in range(n_vars):
             a[i,j,:] = proc[zone].field(1+j*2)
             b[i,j,:] = proc[zone].field(2+j*2)
 
@@ -433,7 +435,7 @@ def _read_excitation(file, ):
 
 
     # Sort the zones from the .tec file
-    zones = proc.keys()
+    zones = list(proc.keys())
     zones.sort()
 
     # Set the frequencies and calculate number of freqs
@@ -446,7 +448,7 @@ def _read_excitation(file, ):
 
     # Populate matrices
     for i, zone in enumerate(zones):
-        for j in xrange(n_vars):
+        for j in range(n_vars):
             a[j,i,:] = proc[zone].field(1+j*2)
             b[j,i,:] = proc[zone].field(2+j*2)