givernylocal 2.3.4__py3-none-any.whl

givernylocal/turbulence_dataset.py

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+########################################################################
+#
+#  Copyright 2024 Johns Hopkins University
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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.
+#
+# Contact: turbulence@pha.jhu.edu
+# Website: http://turbulence.pha.jhu.edu/
+#
+########################################################################
+
+import pathlib
+import numpy as np
+from givernylocal.turbulence_gizmos.basic_gizmos import *
+
+class turb_dataset():
+    def __init__(self, dataset_title = '', output_path = '', auth_token = ''):
+        """
+        initialize the class.
+        """
+        # check that dataset_title is a valid dataset title.
+        check_dataset_title(dataset_title)
+        
+        # turbulence dataset name, e.g. "isotropic8192" or "isotropic1024fine".
+        self.dataset_title = dataset_title
+        
+        # cube size.
+        self.N = get_dataset_resolution(self.dataset_title)
+        # cube spacing (dx, dy, dz).
+        self.spacing = get_dataset_spacing(self.dataset_title)
+        self.dx, self.dy, self.dz = self.spacing
+        
+        # set the directory for saving any output files.
+        self.output_path = output_path.strip()
+        if self.output_path == '':
+            raise Exception("output_path cannot be an empty string ('')")
+        else:
+            self.output_path = pathlib.Path(self.output_path)
+        
+        # create the output directory if it does not already exist.
+        create_output_folder(self.output_path)
+        
+        # user authorization token for pyJHTDB.
+        self.auth_token = auth_token
+    
+    """
+    initialization functions.
+    """
+    def init_constants(self, query_type, var, var_original, var_offsets, timepoint, timepoint_original, sint, sint_specified, tint, option,
+                       num_values_per_datapoint, c):
+        """
+        initialize the constants.
+        """
+        self.var = var
+        self.var_name = var_original
+        self.var_offsets = var_offsets
+        self.timepoint = timepoint
+        self.timepoint_original = timepoint_original
+        self.timepoint_end, self.delta_t = option
+        # sint and sint_specified are the same except for points near the upper and lower z-axis boundaries in
+        # the 'sabl2048*' datasets. for these datasets sint is automatically reduced to an interpolation method
+        # that fits within the z-axis boundary since the z-axis is not periodic. sint_specified will be used for
+        # reading the proper interpolation lookup table(s) from the metadata files.
+        self.sint = sint
+        self.sint_specified = sint_specified
+        self.tint = tint
+        self.num_values_per_datapoint = num_values_per_datapoint
+        self.bytes_per_datapoint = c['bytes_per_datapoint']
+        self.missing_value_placeholder = c['missing_value_placeholder']
+        self.database_file_disk_index = c['database_file_disk_index']
+        self.decimals = c['decimals']
+        self.chunk_size = c['chunk_size']
+        self.file_size = c['file_size']
+        self.query_type = query_type
+        
+        # set the byte order for reading the data from the files.
+        self.dt = np.dtype(np.float32)
+        self.dt = self.dt.newbyteorder('<')
+        
+        # get the number of digits in the timepoint part of the filenames, in order to add leading zeros.
+        self.timepoint_digits = get_timepoint_digits(self.dataset_title)
+        
+        # retrieve the dimension offsets.
+        self.dimension_offsets = get_dataset_dimension_offsets(self.dataset_title, self.var_offsets)
+        
+        # retrieve the coor offsets.
+        self.coor_offsets = get_dataset_coor_offsets(self.dataset_title, self.var_offsets)
+        
+        # set the dataset name to be used in the cutout hdf5 file.
+        self.dataset_name = get_output_variable_name(self.var_name) + '_' + str(self.timepoint_original).zfill(4)
+