Merge pull request #167 from PrincetonUniversity/reader_slice_fix

Analysis script improvements
PrincetonUniversity · Oct 10, 2018 · 5fd9ea5 · 5fd9ea5
2 parents 848a743 + d92b9e5
commit 5fd9ea5
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Showing 2 changed files with 13 additions and 24 deletions.
diff --git a/vis/python/athena_read.py b/vis/python/athena_read.py
@@ -618,11 +618,8 @@ def center_func_3(xm, xp): return 0.5 * (xm + xp)
                         if np.all(self.levels == self.level):
                             self[xf] = np.empty(nx + 1)
                             for n_block in range(int(nx / self.block_size[d-1])):
-                                sample_location = [0, 0, 0]
-                                sample_location[d-1] = n_block
-                                sample_block = np.where(np.all(
-                                    self.logical_locations == sample_location,
-                                    axis=1))[0][0]
+                                sample_block = np.where(self.logical_locations[:, d-1]
+                                                        == n_block)[0][0]
                                 index_low = n_block * self.block_size[d-1]
                                 index_high = index_low + self.block_size[d-1] + 1
                                 self[xf][index_low:index_high] = f[xf][sample_block, :]

diff --git a/vis/python/uniform.py b/vis/python/uniform.py
@@ -1,10 +1,10 @@
+#! /usr/bin/env python
+
 """
 Read .athdf data files and write new ones as single block at constant refinement
 level.
 
 Note: Requires h5py.
-
-Note: Only works for 3D data.
 """
 
 # Python standard modules
@@ -43,10 +43,8 @@ def main(**kwargs):
     for n in file_nums_local:
 
         # Determine filenames
-        input_filename = '{0}.out{1}.{2:05d}.athdf'\
-            .format(kwargs['input_filename'], kwargs['output_num'], n)
-        output_filename = '{0}.out{1}.{2:05d}.athdf'\
-            .format(kwargs['output_filename'], kwargs['output_num'], n)
+        input_filename = '{0}.{1:05d}.athdf'.format(kwargs['input_filename'], n)
+        output_filename = '{0}.{1:05d}.athdf'.format(kwargs['output_filename'], n)
         output_dir, output_base = os.path.split(output_filename)
 
         # Read attributes and data
@@ -63,9 +61,9 @@ def main(**kwargs):
                                  level=level, subsample=subsample)
 
         # Determine new grid size
-        nx1 = attrs['RootGridSize'][0] * 2**level
-        nx2 = attrs['RootGridSize'][1] * 2**level
-        nx3 = attrs['RootGridSize'][2] * 2**level
+        nx1 = attrs['RootGridSize'][0] * 2**level if attrs['MeshBlockSize'][0] > 1 else 1
+        nx2 = attrs['RootGridSize'][1] * 2**level if attrs['MeshBlockSize'][1] > 1 else 1
+        nx3 = attrs['RootGridSize'][2] * 2**level if attrs['MeshBlockSize'][2] > 1 else 1
 
         # Create new HDF5 file
         with h5py.File(output_filename, 'w') as f:
@@ -97,10 +95,8 @@ def main(**kwargs):
 
             # Write datasets
             f.create_dataset('Levels', data=[0], dtype='>i4')
-            f.create_dataset(
-                'LogicalLocations', data=[
-                    0, 0, 0], dtype='>i8', shape=(
-                    1, 3))
+            f.create_dataset('LogicalLocations', data=[0, 0, 0], dtype='>i8',
+                             shape=(1, 3))
             f.create_dataset('x1f', data=data['x1f'], dtype='>f4', shape=(1, nx1 + 1))
             f.create_dataset('x2f', data=data['x2f'], dtype='>f4', shape=(1, nx2 + 1))
             f.create_dataset('x3f', data=data['x3f'], dtype='>f4', shape=(1, nx3 + 1))
@@ -110,9 +106,8 @@ def main(**kwargs):
             var_offset = 0
             for dataset_name, num_vars in zip(
                     f.attrs['DatasetNames'], f.attrs['NumVariables']):
-                f.create_dataset(
-                    dataset_name, dtype='>f4', shape=(
-                        num_vars, 1, nx3, nx2, nx1))
+                f.create_dataset(dataset_name, dtype='>f4',
+                                 shape=(num_vars, 1, nx3, nx2, nx1))
                 for var_num in range(num_vars):
                     variable_name = f.attrs['VariableNames'][var_num + var_offset]
                     f[dataset_name][var_num, 0, :, :, :] = data[variable_name]
@@ -181,9 +176,6 @@ def main(**kwargs):
     parser.add_argument('output_filename',
                         type=str,
                         help='base name of new files to be saved, including directory')
-    parser.add_argument('output_num',
-                        type=int,
-                        help='number of output to convert')
     parser.add_argument('start',
                         type=int,
                         help='first file number to be converted')