Multiple modifications (irregular time steps, etc)

.gitignore

@@ -1,4 +1,4 @@
-.idea/
-venv/
-*.png
-data*
+.idea/
+venv/
+*.png
+data*

LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2019 João Lucas de Sousa Almeida
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2019 João Lucas de Sousa Almeida
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,2 +1,2 @@
-# MLExp
-Basic Python 3 codes aiming at being auxiliary tools for the class IM458 at Unicamp
+# MLExp
+Basic Python 3 codes aiming at being auxiliary tools for the class IM458 at Unicamp

auxiliary/script_pitzDaily.py

@@ -1,90 +1,90 @@
-import numpy as np 
-import os
-from argparse import ArgumentParser 
-import vtk
-from vtk.util.numpy_support import vtk_to_numpy
-import tables 
-
-# Script for reading multiple VTK files and write a HDF5 file. 
-def name_index(input_string):
-
-    strings = input_string.split("_")
-    index = strings[-1]
-    index = int(index) 
-
-    return index
-
-parser = ArgumentParser(description='Argument parsers')
-parser.add_argument('--path', type=str)
-
-args = parser.parse_args()
-
-path = args.path
-
-items = [path + ii for ii in os.listdir(path)]
-data_directories = list(filter(os.path.isdir, items))
-
-data_directories = sorted(data_directories, key=name_index)
-
-variables = {3: 'k', 4: 'nut', 5: 'p', 8: 'rho', 1: 'T', 9: 'U'}
-n_variables = len(variables.keys()) + 2
-
-variables_dict = {var:list()  for var in variables.values()}
-
-number_of_snapshots = len(data_directories)
-
-# Reading the information about the number of cells 
-directory = data_directories[1]
-vtu_file = directory + "\\"+"internal.vtu"
-print("File {} read".format(vtu_file))
-
-reader = vtk.vtkXMLUnstructuredGridReader()
-reader.SetFileName(vtu_file)
-reader.Update()
-data = reader.GetOutput()
-n_cells = data.GetNumberOfCells()
-
-n_cells = data.GetNumberOfCells()
-cells_dict = dict() 
-
-for cell_id in range(n_cells):
-
-    cell = data.GetCell(cell_id)
-    points = vtk_to_numpy(cell.GetPoints().GetData())
-    cells_dict[cell_id] = points.mean(0)
-    print("Cell {} read".format(cell_id))
-
-hdf5_path = path + 'PitzDaily.hdf5'
-
-# Creating the HDF5 file
-h5f = tables.open_file(hdf5_path, mode='w')
-#atom = tables.Atom.from_dtype(np.float64)
-ds = h5f.create_array(h5f.root, 'AllData', np.empty((number_of_snapshots, n_cells, n_variables)))
-
-for ss, directory in enumerate(data_directories[1:]): 
-
-    vtu_file = directory + "\\"+"internal.vtu"
-    print("File {} read".format(vtu_file))
-
-    reader = vtk.vtkXMLUnstructuredGridReader()
-    reader.SetFileName(vtu_file)
-    reader.Update()
-    data = reader.GetOutput()
-
-    print("File {} readed".format(vtu_file))
-
-    variables_list = list() 
-
-    for ii, name in variables.items():
-
-        array = vtk_to_numpy(data.GetCellData().GetArray(ii))
-        if len(array.shape) ==1: array = array[:,None]
-        variables_list.append(array) 
-        print("Variable {} readed".format(name))
-
-    variables_array = np.hstack(variables_list)
-    ds[ss, :, :] = variables_array 
-
-h5f.close()  
-
-print("Input arguments read")
+import numpy as np 
+import os
+from argparse import ArgumentParser 
+import vtk
+from vtk.util.numpy_support import vtk_to_numpy
+import tables 
+
+# Script for reading multiple VTK files and write a HDF5 file. 
+def name_index(input_string):
+
+    strings = input_string.split("_")
+    index = strings[-1]
+    index = int(index) 
+
+    return index
+
+parser = ArgumentParser(description='Argument parsers')
+parser.add_argument('--path', type=str)
+
+args = parser.parse_args()
+
+path = args.path
+
+items = [path + ii for ii in os.listdir(path)]
+data_directories = list(filter(os.path.isdir, items))
+
+data_directories = sorted(data_directories, key=name_index)
+
+variables = {3: 'k', 4: 'nut', 5: 'p', 8: 'rho', 1: 'T', 9: 'U'}
+n_variables = len(variables.keys()) + 2
+
+variables_dict = {var:list()  for var in variables.values()}
+
+number_of_snapshots = len(data_directories)
+
+# Reading the information about the number of cells 
+directory = data_directories[1]
+vtu_file = directory + "\\"+"internal.vtu"
+print("File {} read".format(vtu_file))
+
+reader = vtk.vtkXMLUnstructuredGridReader()
+reader.SetFileName(vtu_file)
+reader.Update()
+data = reader.GetOutput()
+n_cells = data.GetNumberOfCells()
+
+n_cells = data.GetNumberOfCells()
+cells_dict = dict() 
+
+for cell_id in range(n_cells):
+
+    cell = data.GetCell(cell_id)
+    points = vtk_to_numpy(cell.GetPoints().GetData())
+    cells_dict[cell_id] = points.mean(0)
+    print("Cell {} read".format(cell_id))
+
+hdf5_path = path + 'PitzDaily.hdf5'
+
+# Creating the HDF5 file
+h5f = tables.open_file(hdf5_path, mode='w')
+#atom = tables.Atom.from_dtype(np.float64)
+ds = h5f.create_array(h5f.root, 'AllData', np.empty((number_of_snapshots, n_cells, n_variables)))
+
+for ss, directory in enumerate(data_directories[1:]): 
+
+    vtu_file = directory + "\\"+"internal.vtu"
+    print("File {} read".format(vtu_file))
+
+    reader = vtk.vtkXMLUnstructuredGridReader()
+    reader.SetFileName(vtu_file)
+    reader.Update()
+    data = reader.GetOutput()
+
+    print("File {} readed".format(vtu_file))
+
+    variables_list = list() 
+
+    for ii, name in variables.items():
+
+        array = vtk_to_numpy(data.GetCellData().GetArray(ii))
+        if len(array.shape) ==1: array = array[:,None]
+        variables_list.append(array) 
+        print("Variable {} readed".format(name))
+
+    variables_array = np.hstack(variables_list)
+    ds[ss, :, :] = variables_array 
+
+h5f.close()  
+
+print("Input arguments read")