Merge pull request #105 from brittonsmith/infinity

Be more careful about limiting size of line deposition array.

.travis.yml

@@ -20,9 +20,9 @@ env:
     TRIDENT_ION_DATA=$HOME/.trident
     TRIDENT_ANSWER_DATA=$HOME/answer_test_data
     TRIDENT_CONFIG=$TRIDENT_ION_DATA/config.tri
-    YT_GOLD=4f56c4c9b534106fd45e8dfe644280755236fb5d
+    YT_GOLD=3b7ad0cf0e0c4002137100ac22557027d4811273
     YT_HEAD=yt-4.0
-    TRIDENT_GOLD=test-standard-sph-viz-v3
+    TRIDENT_GOLD=test-standard-sph-viz-v4
 
 before_install:
   - |

trident/absorption_spectrum/absorption_spectrum.py

@@ -464,6 +464,10 @@ def make_spectrum(self, input_object, output_file=None,
             input_ds = input_object.ds
             field_data = input_object
 
+        # temporary fix for yt-4.0 ytdata selection issue
+        input_ds.domain_left_edge = input_ds.domain_left_edge.to('code_length')
+        input_ds.domain_right_edge = input_ds.domain_right_edge.to('code_length')
+
         if self.bin_space == 'velocity':
             self.zero_redshift = getattr(input_ds, 'current_redshift', 0)
 
@@ -852,7 +856,9 @@ def _add_lines_to_spectrum(self, field_data, use_peculiar_velocity,
                       self._get_bin_indices(
                           my_lambda, self.bin_width,
                           my_obs[i], window_width_in_bins)
-                    n_vbins = window_width_in_bins * n_vbins_per_bin[i]
+
+                    window_size = right_index - left_index
+                    n_vbins = window_size * n_vbins_per_bin[i]
 
                     # the array of virtual bins in lambda space
                     vbins = \
@@ -869,6 +875,12 @@ def _add_lines_to_spectrum(self, field_data, use_peculiar_velocity,
                     else:
                         raise RuntimeError('What bin_space is this?')
 
+                    if my_vbins.size > 1e6:
+                        mylog.warning(
+                            ('About to deposit a line with %d bins.' +
+                             'This may take a while. You might want to consider ' +
+                             'increasing the bin size.') % my_vbins.size)
+
                     # the virtual bins and their corresponding opacities
                     my_vbins, vtau = \
                         tau_profile(
@@ -889,6 +901,16 @@ def _add_lines_to_spectrum(self, field_data, use_peculiar_velocity,
                                   my_obs[i], window_width_in_bins)
 
                         break
+
+                    # If we have fixed bins, call it done when the
+                    # spectrum takes up the entire range.
+                    if not self._auto_lambda:
+                        left_ok = vtau[0] < min_tau or left_index <= 0
+                        right_ok = vtau[-1] < min_tau or \
+                          right_index >= self.lambda_field.size
+                        if left_ok and right_ok:
+                            break
+
                     window_width_in_bins *= 2
 
                 if center_index is None:
@@ -1041,6 +1063,18 @@ def _get_bin_indices(self, lambda_field, dlambda, lambda_obs,
         left_index = (center_index - window_width_in_bins//2)
         right_index = (center_index + window_width_in_bins//2)
 
+        # if fixed size, make some sensible bounds on size of virtual spectrum
+        if not self._auto_lambda:
+            if left_index <= 0 and right_index >= lambda_field.size:
+                left_index = 0
+                right_index = lambda_field.size
+            elif center_index < 0:
+                left_index = max(left_index, center_index)
+                right_index = min(right_index, lambda_field.size)
+            elif center_index > lambda_field.size:
+                left_index = max(left_index, 0)
+                right_index = min(right_index, center_index)
+
         return left_index, center_index, right_index
 
     def _get_global_lambda_field(self, comm=None):

trident/light_ray.py

@@ -712,6 +712,11 @@ def make_light_ray(self, seed=None, periodic=True,
         if data_filename is not None:
             self._write_light_ray(data_filename, all_data)
             ray_ds = load(data_filename)
+
+            # temporary fix for yt-4.0 ytdata selection issue
+            ray_ds.domain_left_edge = ray_ds.domain_left_edge.to('code_length')
+            ray_ds.domain_right_edge = ray_ds.domain_right_edge.to('code_length')
+
             return ray_ds
         else:
             return None

trident/spectrum_generator.py

@@ -369,6 +369,10 @@ def make_spectrum(self, ray, lines='all',
         else:
             raise RuntimeError("Unrecognized ray type.")
 
+        # temporary fix for yt-4.0 ytdata selection issue
+        ray.domain_left_edge = ray.domain_left_edge.to('code_length')
+        ray.domain_right_edge = ray.domain_right_edge.to('code_length')
+
         # Clear out any previous spectrum that existed first
         self.clear_spectrum()
 

trident/utilities.py

@@ -444,6 +444,11 @@ def make_onezone_ray(density=1e-26, temperature=1000, metallicity=0.3,
 
     # load dataset and make spectrum
     ray = load(filename)
+
+    # temporary fix for yt-4.0 ytdata selection issue
+    ray.domain_left_edge = ray.domain_left_edge.to('code_length')
+    ray.domain_right_edge = ray.domain_right_edge.to('code_length')
+
     return ray
 
 def import_check():