V24.1

.gitignore

@@ -1,5 +1,7 @@
 # Excluded files
 *.db
+*.csv
+*.json
 
 # Excluded folders
 .idea

README.md

@@ -3,7 +3,7 @@
 ![logo](docs/src/_static/images/logo.svg)
 
 The **SSD** project provides Python3 tools allowing users to easily develop **data storage** and **visualization** 
-strategies for their **numerical simulations** with az minimal lines of code.
+strategies for their **numerical simulations** with a minimal lines of code.
 
 This project has two main objectives:
 * Easy **storage** management system for **any data** from a numerical simulation;

docs/src/Core/Rendering/api.rst

@@ -1,25 +1,17 @@
 API
 ===
 
-UserAPI
--------
 
-.. autoclass:: SSD.Core.Rendering.UserAPI.UserAPI
+.. autoclass:: SSD.Core.Rendering.user_api.UserAPI
     :special-members: __init__
     :members:
 
 
-Visualizer
-----------
-
-.. autoclass:: SSD.Core.Rendering.Visualizer.Visualizer
+.. autoclass:: SSD.Core.Rendering.visualizer.Visualizer
     :special-members: __init__
     :members:
 
 
-Replay
-------
-
-.. autoclass:: SSD.Core.Rendering.Replay.Replay
+.. autoclass:: SSD.Core.Rendering.replay.Replay
     :special-members: __init__
     :members:

docs/src/Core/Storage/api.rst

@@ -1,10 +1,8 @@
 API
 ===
 
-Database
---------
 
-.. autoclass:: SSD.Core.Storage.Database.Database
+.. autoclass:: SSD.Core.Storage.database.Database
     :special-members: __init__
     :members:
 

docs/src/Core/Storage/database.rst

@@ -9,7 +9,7 @@ To create this file with a `.db` extension, a call to the ``new`` method is requ
 
 .. code-block:: python
 
-    from SSD.Core import Database
+    from SSD.Core.Storage import Database
 
     # Create a new Database object and a new storage file
     db = Database(database_dir='my_directory',
@@ -28,7 +28,7 @@ Loading an existing *Database* is pretty similar as creating a new one, except t
 
 .. code-block:: python
 
-    from SSD.Core import Database
+    from SSD.Core.Storage import Database
 
     # Create a new Database object and load an exiting storage file
     db = Database(database_dir='my_directory',
@@ -107,7 +107,7 @@ The following *Field* types are available:
     +--------------+--------------------------------------+---------------------------------------------------------------------------------------+
     | ``bool``     | :guilabel:`bool`                     | `BooleanField <http://docs.peewee-orm.com/en/latest/peewee/api.html#BooleanField>`_   |
     +--------------+--------------------------------------+---------------------------------------------------------------------------------------+
-    | ``ndarray``  | :guilabel:`import numpy.ndarray`     | See ``AdaptiveDB/ExtendedFields.py``                                                  |
+    | ``ndarray``  | :guilabel:`import numpy.ndarray`     | Field class for storing numpy arrays.                                                 |
     +--------------+--------------------------------------+---------------------------------------------------------------------------------------+
     | ``datetime`` | :guilabel:`import datetime.datetime` | `DateTimeField <http://docs.peewee-orm.com/en/latest/peewee/api.html#DateTimeField>`_ |
     +--------------+--------------------------------------+---------------------------------------------------------------------------------------+

docs/src/Core/Storage/utils.rst

@@ -10,10 +10,10 @@ Each *Table* from all *Databases* will be duplicated in the new *Database*; in t
 
 .. code-block:: python
 
-    from SSD.Core import merge
+    from SSD.Core.Storage import merge
 
-    merge(database_names=['my_Database1', 'my_Database2'],
-          new_database_name='my_MergedDatabase',
+    merge(database_files=['my_Database1', 'my_Database2'],
+          new_database_file='my_MergedDatabase',
           remove_existing=True)
     """
     >> DATABASE my_Database1.db
@@ -51,7 +51,9 @@ Each *Table* from all *Databases* will be duplicated in the new *Database*; in t
             - _dt_ (DATETIME) (default)
             - my_Data (FLOAT)
 
-    >> Confirm new Database architecture ? (y/n):
+    >> Confirm new Database architecture ? (y/n): y
+    Proceeding...
+    Merge complete.
     """
 
 
@@ -63,9 +65,9 @@ Both methods require tuples defines as :guilabel:`(current_name, new_name)`:
 
 .. code-block:: python
 
-    from SSD.Core import rename_tables, rename_fields
+    from SSD.Core.Storage import rename_tables, rename_fields
 
-    rename_tables(database_name='my_Database',
+    rename_tables(database_file='my_Database',
                   renamed_tables=[('my_StoringTable', 'my_NewStoringTable'), ('my_ExchangeTable', 'my_NewExchangeTable')])
     """
     >> DATABASE my_Database.db
@@ -80,7 +82,7 @@ Both methods require tuples defines as :guilabel:`(current_name, new_name)`:
             - my_Data (FLOAT)
     """
 
-    rename_fields(database_name='my_Database',
+    rename_fields(database_file='my_Database',
                   table_name='my_NewStoringTable',
                   renamed_fields=('my_Condition', 'my_Test'))
     """
@@ -104,7 +106,7 @@ The ``remove_tables`` and ``remove_fields`` tools allows users to remove *Tables
 
 .. code-block:: python
 
-    from SSD.Core import remove_tables, remove_fields
+    from SSD.Core.Storage import remove_tables, remove_fields
 
     rename_tables(database_name='my_Database',
                   remove_tables='my_ExchangeTable')
@@ -135,7 +137,7 @@ The ``export`` tool allows users to export a *Database* either in CSV format eit
 
 .. code-block:: python
 
-    from SSD.Core import export
+    from SSD.Core.Storage import export
 
     export(database_name='my_Database',
            exporter='csv',

docs/src/SOFA/api.rst

@@ -4,36 +4,26 @@ API
 Storage
 -------
 
-Database
-""""""""
 
-.. autoclass:: SSD.SOFA.Storage.Database.Database
+.. autoclass:: SSD.SOFA.Storage.database.Database
     :special-members: __init__
     :members:
 
 
 Rendering
 ---------
 
-UserAPI
-"""""""
 
-.. autoclass:: SSD.SOFA.Rendering.UserAPI.UserAPI
+.. autoclass:: SSD.SOFA.Rendering.user_api.UserAPI
     :special-members: __init__
     :members:
 
 
-Visualizer
-""""""""""
-
-.. autoclass:: SSD.SOFA.Rendering.Visualizer.Visualizer
+.. autoclass:: SSD.SOFA.Rendering.visualizer.Visualizer
     :special-members: __init__
     :members:
 
 
-Replay
-""""""
-
-.. autoclass:: SSD.SOFA.Rendering.Replay.Replay
+.. autoclass:: SSD.SOFA.Rendering.replay.Replay
     :special-members: __init__
     :members:

docs/src/SOFA/rendering.rst

@@ -46,7 +46,7 @@ It is also possible to create and update objects manually such as in the ``Core`
         .. code-block:: python
 
             import Sofa
-            from SSD.SOFA import UserAPI
+            from SSD.SOFA.Rendering import UserAPI
 
             # Create the root node
             root = Sofa.Core.Node('root')
@@ -87,7 +87,7 @@ It is also possible to create and update objects manually such as in the ``Core`
 
         .. code-block:: python
 
-            from SSD.SOFA import UserAPI
+            from SSD.SOFA.Rendering import UserAPI
 
             def createScene(root):
 

docs/src/SOFA/storage.rst

@@ -38,7 +38,7 @@ Adding callbacks is very simple, since you only have to specify:
         .. code-block:: python
 
             import Sofa
-            from SSD.SOFA import Database
+            from SSD.SOFA.Storage import Database
 
             # Create the root node
             root = Sofa.Core.Node('root')
@@ -76,7 +76,7 @@ Adding callbacks is very simple, since you only have to specify:
 
         .. code-block:: python
 
-            from SSD.SOFA import Database
+            from SSD.SOFA.Storage import Database
 
             def createScene(root):
 

examples/Core/rendering/README.md

@@ -6,7 +6,8 @@ It is recommended to inspect and run the python scripts following this order:
 
 * ``visualization.py``: discover all visual object types (how to create and update them).
 * ``replay.py``: how to replay a simulation from a *Database*.
-* ``<backend>_offscreen.py``: an example of offscreen rendering.
+* ``offscreen.py``: an example of off-screen rendering.
 * ``several_factories.py``: how to manage several *Factories* with a single *Visualizer*.
+* ``several_factories_offsceen.py``: how to manage several *Factories* with a single *Visualizer* in off-screen mode.
 
 Run the examples using ``python3 <example_name>.py <backend>`` with backend being either 'vedo' (by default) or 'open3d'.

examples/Core/rendering/offscreen.py

@@ -2,48 +2,51 @@
 from numpy.random import random
 from sys import argv
 
-from SSD.Core import UserAPI, Replay
+from SSD.Core.Rendering import UserAPI, Replay
 
 # 1. Create the visualization API
-factory = UserAPI(database_name='offscreen',
+factory = UserAPI(database_dir='my_databases',
+                  database_name='offscreen',
                   remove_existing=True)
 
 # 2. Create the object to render
-armadillo = Mesh('armadillo.obj')
+mesh = Mesh('armadillo.obj').compute_normals()
 
 # 3. Add objects to the Visualizer
 # 3.1. Add a Mesh (object_id = 0)
-factory.add_mesh(positions=armadillo.points(),
-                 cells=armadillo.cells(),
+factory.add_mesh(positions=mesh.vertices,
+                 cells=mesh.cells,
                  at=0,
                  alpha=0.8,
                  c='orange6',
                  wireframe=False,
                  line_width=0.)
 # 3.2. Add a PointCloud (object_id = 1)
-factory.add_points(positions=armadillo.points(),
+factory.add_points(positions=mesh.vertices,
                    at=1,
                    point_size=5,
-                   scalar_field=armadillo.points()[:, 1])
+                   scalar_field=mesh.vertices[:, 1])
 
 # 4. Initialize the visualization
 factory.launch_visualizer(offscreen=True)
 
 # 5. Run a few steps
 print('Running offscreen...')
 for step in range(100):
-    updated_armadillo = armadillo.clone().points(armadillo.points() + 0.1 * random(armadillo.points().shape))
+    updated_mesh = mesh.clone()
+    updated_mesh.vertices = mesh.vertices + 0.1 * random(mesh.vertices.shape)
     # 5.1. Update the Mesh
     factory.update_mesh(object_id=0,
-                        positions=updated_armadillo.points())
+                        positions=updated_mesh.vertices)
     # 5.2. Update the PointCloud
     factory.update_points(object_id=1,
-                          positions=updated_armadillo.points())
+                          positions=updated_mesh.vertices)
     # 5.3. Call a rendering step
     factory.render()
 
 # 6. Close the visualization, replay steps
 print('...then replay.')
 factory.close()
-Replay(database_name='offscreen',
+Replay(database_dir='my_databases',
+       database_name='offscreen',
        backend='vedo' if len(argv) == 1 else argv[1]).launch()

examples/Core/rendering/replay.py

@@ -1,12 +1,14 @@
 from os.path import exists
+from os import system
 from sys import argv
 
-from SSD.Core import Replay
+from SSD.Core.Rendering import Replay
 
 # Check Database existence
-if not exists('visualization.db'):
-    raise FileNotFoundError("You must create the Database using `python3 visualization.py` before to replay it.")
+if not exists('my_databases/visualization.db'):
+    system('python3 visualization.py')
 
 # Launch replay
-Replay(database_name='visualization',
+Replay(database_dir='my_databases',
+       database_name='visualization',
        backend='vedo' if len(argv) == 1 else argv[1]).launch()

examples/Core/rendering/several_factories.py

@@ -3,7 +3,8 @@
 from threading import Thread
 from sys import argv
 
-from SSD.Core import Database, UserAPI, Visualizer
+from SSD.Core.Storage import Database
+from SSD.Core.Rendering import UserAPI, Visualizer
 
 
 class Simulation:
@@ -13,12 +14,12 @@ def __init__(self,
                  idx_instance: int):
 
         # Create the Mesh object
-        self.armadillo = Mesh('armadillo.obj')
+        self.mesh = Mesh('armadillo.obj')
         # Create a Factory and add the Mesh object
         self.factory = UserAPI(database=database,
                                idx_instance=idx_instance)
-        self.factory.add_mesh(positions=self.armadillo.points(),
-                              cells=self.armadillo.cells(),
+        self.factory.add_mesh(positions=self.mesh.vertices,
+                              cells=self.mesh.cells,
                               at=idx_instance,
                               c='orange3' if idx_instance == 0 else 'blue3')
 
@@ -30,7 +31,7 @@ def connect_to_visualizer(self):
     def step(self):
 
         # Update the Mesh positions
-        updated_positions = self.armadillo.points() + 0.1 * random(self.armadillo.points().shape)
+        updated_positions = self.mesh.vertices + 0.1 * random(self.mesh.vertices.shape)
         self.factory.update_mesh(object_id=0,
                                  positions=updated_positions)
         self.factory.render()
@@ -44,7 +45,8 @@ def close(self):
 if __name__ == '__main__':
 
     # 1. Create a new Database
-    db = Database(database_name='several_factories').new(remove_existing=True)
+    db = Database(database_dir='my_databases',
+                  database_name='several_factories').new(remove_existing=True)
 
     # 2. Create several simulations
     nb_simu = 2
@@ -54,6 +56,7 @@ def close(self):
     # 3. Connect a single Visualizer to the Factories
     # 3.1. Create a new Visualizer
     Visualizer.launch(backend='vedo' if len(argv) == 1 else argv[1],
+                      database_dir='my_databases',
                       database_name='several_factories',
                       nb_clients=nb_simu)
     # 3.2. Connect each Factory to the Visualizer (must be launched in thread)