io

plantdb.commons.io

The io module of the ROMI plantdb library contains all functions for reading and writing data to database.

Hereafter we detail the formats and their associated Python types and meanings.

json

Dictionaries or lists, read and written using json.

• Python objects: dict, list
• File extensions: 'json'

toml

Dictionaries or lists, read and written using toml.

• Python objects: dict, list
• File extensions: 'toml'

2D image

RGB or RGBA image data, read and written using imageio.

• Python objects: numpy.ndarray
• File extensions: 'jpg', 'png'

3D volume

Grayscale or binary volume image data, read and written using imageio.

• Python objects: numpy.ndarray
• File extensions: 'tiff'

Labelled 3D volume

Labelled volume image data, converted to dictionary of 3D (binary) numpy arrays, read and written using numpy.

• Python objects: dict of 3D numpy.ndarray
• File extensions: 'npz'

Point cloud

Point clouds, read and written using open3d.

• Python object: open3d.geometry.PointCloud
• File extensions: 'ply'

Triangle mesh

Triangular meshes, read and written using open3d.

• Python object: open3d.geometry.TriangleMesh
• File extensions: 'ply'

Voxel grid

Voxel grids, read and written using open3d.

• Python object: open3d.geometry.VoxelGrid
• File extensions: 'ply'

Tree graph

Tree graphs, read and written using networkx.

• Python object: networkx.Graph
• File extensions: 'p'

Pytorch tensor

Trained tensor, read and written using torch.

• Python object: torch.tensor
• File extensions: 'pt'

read_graph

read_graph(file, **kwargs)

Reads a networkx Graph from a ROMI database file or a path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	A File instance or file path, to read from.	required
ext	str	File extension, defaults to "p".	required

Returns:

Type	Description
Graph	The loaded (tree) graph object.

Examples:

>>> import networkx as nx
>>> from plantdb.commons.io import read_graph, write_graph
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file("test_nx_graph")
>>> g = nx.path_graph(4)
>>> print(g)
Graph with 4 nodes and 3 edges
>>> write_graph(f, g)
>>> f = fs.get_file("test_nx_graph")
>>> g2 = read_graph(f)
>>> print(g2)
Graph with 4 nodes and 3 edges

Source code in plantdb/commons/io.py

def read_graph(file, **kwargs):
    """Reads a networkx ``Graph`` from a ROMI database file or a path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        A ``File`` instance or file path, to read from.
    ext : str, optional
        File extension, defaults to "p".

    Returns
    -------
    networkx.Graph
        The loaded (tree) graph object.

    Examples
    --------
    >>> import networkx as nx
    >>> from plantdb.commons.io import read_graph, write_graph
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file("test_nx_graph")
    >>> g = nx.path_graph(4)
    >>> print(g)
    Graph with 4 nodes and 3 edges
    >>> write_graph(f, g)
    >>> f = fs.get_file("test_nx_graph")
    >>> g2 = read_graph(f)
    >>> print(g2)
    Graph with 4 nodes and 3 edges
    """
    import pickle
    # Get path to file if in a database:
    if isinstance(file, fsdb.File):
        file = file.path()
    # Load the pickled file:
    with open(file, mode='rb') as f:
        G = pickle.load(f, **kwargs)
    return G

read_image

read_image(file, **kwargs)

Reads a 2D image from a ROMI database file or a path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	A File instance or file path, to read from.	required

Returns:

Type	Description
ndarray	The image as an RGB(A) array.

Examples:

>>> import numpy as np
>>> from plantdb.commons.io import read_image, write_image
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file("test_image")
>>> rng = np.random.default_rng()
>>> img = np.array(rng.random((5, 5, 3))*255, dtype='uint8')  # an 8bit 5x5 RGB image
>>> write_image(f, img)
>>> f = fs.get_file("test_image")
>>> img2 = read_image(f)
>>> np.testing.assert_array_equal(img, img2)  # raise an exception if not equal!

Source code in plantdb/commons/io.py

def read_image(file, **kwargs):
    """Reads a 2D image from a ROMI database file or a path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        A ``File`` instance or file path, to read from.

    Returns
    -------
    numpy.ndarray
        The image as an RGB(A) array.

    Examples
    --------
    >>> import numpy as np
    >>> from plantdb.commons.io import read_image, write_image
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file("test_image")
    >>> rng = np.random.default_rng()
    >>> img = np.array(rng.random((5, 5, 3))*255, dtype='uint8')  # an 8bit 5x5 RGB image
    >>> write_image(f, img)
    >>> f = fs.get_file("test_image")
    >>> img2 = read_image(f)
    >>> np.testing.assert_array_equal(img, img2)  # raise an exception if not equal!
    """
    import imageio.v3 as iio
    # Get path to file if in a database:
    if isinstance(file, fsdb.File):
        file = file.path()
    return iio.imread(file, **kwargs)

read_json

read_json(file, **kwargs)

Reads a JSON from a ROMI database file or a path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	A File instance or file path, to read from.	required

Returns:

Type	Description
dict	The deserialized JSON file.

Examples:

>>> from plantdb.commons.io import read_json, write_json
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file("test_json")
>>> data = {"test": False, 'ROMI': 'RObotics for MIcrofarms'}
>>> write_json(f, data)
>>> f = fs.get_file("test_json")
>>> read_json(f)
{'test': False, 'ROMI': 'RObotics for MIcrofarms'}

Source code in plantdb/commons/io.py

def read_json(file, **kwargs):
    """Reads a JSON from a ROMI database file or a path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        A ``File`` instance or file path, to read from.

    Returns
    -------
    dict
        The deserialized JSON file.

    Examples
    --------
    >>> from plantdb.commons.io import read_json, write_json
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file("test_json")
    >>> data = {"test": False, 'ROMI': 'RObotics for MIcrofarms'}
    >>> write_json(f, data)
    >>> f = fs.get_file("test_json")
    >>> read_json(f)
    {'test': False, 'ROMI': 'RObotics for MIcrofarms'}
    """
    import json
    # Get path to file if in a database:
    if isinstance(file, fsdb.File):
        file = file.path()
    # Load the file:
    with open(file, mode='r') as f:
        data = json.loads(f.read(), **kwargs)
    return data

read_npz

read_npz(file, **kwargs)

Reads a dictionary of arrays from a ROMI database file or a path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	A File instance or file path, to read from.	required

Returns:

Type	Description
dict of numpy.ndarray	The dictionary of numpy arrays.

Examples:

>>> import numpy as np
>>> from plantdb.commons.io import read_npz, write_npz
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file('test_npz')
>>> rng = np.random.default_rng()
>>> npz = {f"{i}": rng.random((10, 10, 3)) for i in range(5)}
>>> write_npz(f, npz)
>>> f = fs.get_file("test_npz")
>>> npz2 = read_npz(f)
>>> np.testing.assert_array_equal(npz["0"], npz2["0"])  # raise an exception if not equal!

Source code in plantdb/commons/io.py

def read_npz(file, **kwargs):
    """Reads a dictionary of arrays from a ROMI database file or a path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        A ``File`` instance or file path, to read from.

    Returns
    -------
    dict of numpy.ndarray
        The dictionary of numpy arrays.

    Examples
    --------
    >>> import numpy as np
    >>> from plantdb.commons.io import read_npz, write_npz
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file('test_npz')
    >>> rng = np.random.default_rng()
    >>> npz = {f"{i}": rng.random((10, 10, 3)) for i in range(5)}
    >>> write_npz(f, npz)
    >>> f = fs.get_file("test_npz")
    >>> npz2 = read_npz(f)
    >>> np.testing.assert_array_equal(npz["0"], npz2["0"])  # raise an exception if not equal!
    """
    import numpy as np
    # Get path to file if in a database:
    if isinstance(file, fsdb.File):
        file = file.path()
    return dict(np.load(file, **kwargs))

read_point_cloud

read_point_cloud(file, **kwargs)

Reads a point cloud from a ROMI database file or a path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	A File instance or file path, to read from.	required

Returns:

Type	Description
PointCloud	The loaded point cloud object.

Examples:

>>> import open3d as o3d
>>> import numpy as np
>>> from plantdb.commons.io import read_point_cloud, write_point_cloud
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file('test_npz')
>>> pcd = o3d.geometry.PointCloud()
>>> pcd.points = o3d.utility.Vector3dVector(np.array([[1, 2, 3]]))
>>> write_point_cloud(f,pcd)
>>> f = fs.get_file('test_npz')
>>> pcd = read_point_cloud(f)
>>> print(type(pcd))
<class 'open3d.cuda.pybind.geometry.PointCloud'>
>>> print(np.asarray(pcd.points))
[[1. 2. 3.]]

Source code in plantdb/commons/io.py

def read_point_cloud(file, **kwargs):
    """Reads a point cloud from a ROMI database file or a path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        A ``File`` instance or file path, to read from.

    Returns
    -------
    open3d.geometry.PointCloud
        The loaded point cloud object.

    Examples
    --------
    >>> import open3d as o3d
    >>> import numpy as np
    >>> from plantdb.commons.io import read_point_cloud, write_point_cloud
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file('test_npz')
    >>> pcd = o3d.geometry.PointCloud()
    >>> pcd.points = o3d.utility.Vector3dVector(np.array([[1, 2, 3]]))
    >>> write_point_cloud(f,pcd)
    >>> f = fs.get_file('test_npz')
    >>> pcd = read_point_cloud(f)
    >>> print(type(pcd))
    <class 'open3d.cuda.pybind.geometry.PointCloud'>
    >>> print(np.asarray(pcd.points))
    [[1. 2. 3.]]
    """
    from open3d import io
    # Get path to file if in a database:
    if isinstance(file, fsdb.File):
        file = file.path()
    return io.read_point_cloud(str(file), **kwargs)

read_toml

read_toml(file, **kwargs)

Reads a TOML from a ROMI database file or a path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	A File instance or file path, to read from.	required

Returns:

Type	Description
dict	The deserialized TOML file.

Examples:

>>> from plantdb.commons.io import read_toml, write_toml
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file("test_json")
>>> data = {"test": True, 'ROMI': 'RObotics for MIcrofarms'}
>>> write_toml(f, data)
>>> f = fs.get_file("test_json")
>>> read_toml(f)
{'test': True}

Source code in plantdb/commons/io.py

def read_toml(file, **kwargs):
    """Reads a TOML from a ROMI database file or a path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        A ``File`` instance or file path, to read from.

    Returns
    -------
    dict
        The deserialized TOML file.

    Examples
    --------
    >>> from plantdb.commons.io import read_toml, write_toml
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file("test_json")
    >>> data = {"test": True, 'ROMI': 'RObotics for MIcrofarms'}
    >>> write_toml(f, data)
    >>> f = fs.get_file("test_json")
    >>> read_toml(f)
    {'test': True}
    """
    import toml
    # Get path to file if in a database:
    if isinstance(file, fsdb.File):
        file = file.path()
    # Load the file:
    with open(file, mode='r') as f:
        data = toml.loads(f.read(), **kwargs)
    return data

read_torch

read_torch(file, ext='pt', **kwargs)

Reads a torch tensor from a ROMI database file or a path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	A File instance or file path, to read from.	required
ext	str	File extension, defaults to "pt".	'pt'

Returns:

Type	Description
Tensor	The loaded tensor object.

Examples:

>>> from plantdb.commons.io import read_torch
>>> from plantdb.commons.test_database import test_database
>>> db = test_database(with_models=True)
>>> db.connect()
>>> scan = db.get_scan("real_plant_analyzed")
>>> model_file = db.get_scan('models').get_fileset('models').get_file('Resnet_896_896_epoch50')
>>> model = read_torch(model_file)
>>> db.disconnect()

Source code in plantdb/commons/io.py

def read_torch(file, ext="pt", **kwargs):
    """Reads a torch tensor from a ROMI database file or a path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        A ``File`` instance or file path, to read from.
    ext : str, optional
        File extension, defaults to "pt".

    Returns
    -------
    Torch.Tensor
        The loaded tensor object.

    Examples
    --------
    >>> from plantdb.commons.io import read_torch
    >>> from plantdb.commons.test_database import test_database
    >>> db = test_database(with_models=True)
    >>> db.connect()
    >>> scan = db.get_scan("real_plant_analyzed")
    >>> model_file = db.get_scan('models').get_fileset('models').get_file('Resnet_896_896_epoch50')
    >>> model = read_torch(model_file)
    >>> db.disconnect()
    """
    import torch
    # Get path to file if in a database:
    if isinstance(file, fsdb.File):
        file = file.path()
    return torch.load(file, **kwargs)

read_triangle_mesh

read_triangle_mesh(file, **kwargs)

Reads a triangular mesh from a ROMI database file or a path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	A File instance or file path, to read from.	required

Returns:

Type	Description
TriangleMesh	The loaded triangular mesh object.

Source code in plantdb/commons/io.py

def read_triangle_mesh(file, **kwargs):
    """Reads a triangular mesh from a ROMI database file or a path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        A ``File`` instance or file path, to read from.

    Returns
    -------
    open3d.geometry.TriangleMesh
        The loaded triangular mesh object.
    """
    from open3d import io
    # Get path to file if in a database:
    if isinstance(file, fsdb.File):
        file = file.path()
    return io.read_triangle_mesh(str(file), **kwargs)

read_volume

read_volume(file, ext='tiff', **kwargs)

Reads a volume image from a ROMI database file or a path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	A File instance or file path, to read from.	required
ext	str	File extension, defaults to "tiff".	'tiff'

Returns:

Type	Description
ndarray	The volume as a 3D array.

Examples:

>>> import numpy as np
>>> from plantdb.commons.io import read_volume, write_volume
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file('test_volume')
>>> rng = np.random.default_rng()
>>> vol = rng.random((50, 10, 10))
>>> write_volume(f, vol)
>>> f = fs.get_file("test_volume")
>>> vol2 = read_volume(f)
>>> np.testing.assert_array_equal(vol, vol2)  # raise an exception if not equal!

Source code in plantdb/commons/io.py

def read_volume(file, ext="tiff", **kwargs):
    """Reads a volume image from a ROMI database file or a path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        A ``File`` instance or file path, to read from.
    ext : str, optional
        File extension, defaults to "tiff".

    Returns
    -------
    numpy.ndarray
        The volume as a 3D array.

    Examples
    --------
    >>> import numpy as np
    >>> from plantdb.commons.io import read_volume, write_volume
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file('test_volume')
    >>> rng = np.random.default_rng()
    >>> vol = rng.random((50, 10, 10))
    >>> write_volume(f, vol)
    >>> f = fs.get_file("test_volume")
    >>> vol2 = read_volume(f)
    >>> np.testing.assert_array_equal(vol, vol2)  # raise an exception if not equal!
    """
    import imageio.v3 as iio
    # Get path to file if in a database:
    if isinstance(file, fsdb.File):
        file = file.path()
    return iio.imread(file, **kwargs)

read_voxel_grid

read_voxel_grid(file, **kwargs)

Reads a voxel grid from a ROMI database file or a path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	A File instance or file path, to read from.	required

Returns:

Type	Description
VoxelGrid	The loaded point cloud object.

Source code in plantdb/commons/io.py

def read_voxel_grid(file, **kwargs):
    """Reads a voxel grid from a ROMI database file or a path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        A ``File`` instance or file path, to read from.

    Returns
    -------
    open3d.geometry.VoxelGrid
        The loaded point cloud object.
    """
    from open3d import io
    # Get path to file if in a database:
    if isinstance(file, fsdb.File):
        file = file.path()
    return io.read_voxel_grid(str(file), **kwargs)

write_graph

write_graph(file, data, ext='p', **kwargs)

Writes a networkx Graph to a ROMI database file.

Parameters:

Name	Type	Description	Default
file	File or Path or str	If a File instance, the file will be saved to the associated database/scan/fileset. Else, write the data to the given file path, ignoring the extension parameter ext.	required
data	Graph	The (tree) graph object to save.	required
ext	str	File extension, defaults to "p".	'p'

Examples:

>>> import networkx as nx
>>> from plantdb.commons.io import write_graph
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file("test_nx_graph")
>>> g = nx.path_graph(4)
>>> write_graph(f, g)

Source code in plantdb/commons/io.py

def write_graph(file, data, ext="p", **kwargs):
    """Writes a networkx ``Graph`` to a ROMI database file.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        If a ``File`` instance, the file will be saved to the associated database/scan/fileset.
        Else, write the `data` to the given file path, ignoring the extension parameter `ext`.
    data : networkx.Graph
        The (tree) graph object to save.
    ext : str, optional
        File extension, defaults to "p".

    Examples
    --------
    >>> import networkx as nx
    >>> from plantdb.commons.io import write_graph
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file("test_nx_graph")
    >>> g = nx.path_graph(4)
    >>> write_graph(f, g)
    """
    _writer(file, data, ext, _write_graph, **kwargs)
    return

write_image

write_image(file, data, ext='png', **kwargs)

Writes a 2D image to a ROMI database file or to a given path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	If a File instance, the file will be saved to the associated database/scan/fileset. Else, write the data to the given file path, ignoring the extension parameter ext.	required
data	array like	The 2D image (RGB array) to save.	required
ext	(png, jpeg, tiff)	File extension, defaults to "png".	'png'

Examples:

>>> import numpy as np
>>> from plantdb.commons.io import write_image
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file("test_image")
>>> rng = np.random.default_rng()
>>> img = np.array(rng.random((5, 5, 3))*255, dtype='uint8')  # an 8bit 5x5 RGB image
>>> write_image(f, img)

Source code in plantdb/commons/io.py

def write_image(file, data, ext="png", **kwargs):
    """Writes a 2D image to a ROMI database file or to a given path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        If a ``File`` instance, the file will be saved to the associated database/scan/fileset.
        Else, write the `data` to the given file path, ignoring the extension parameter `ext`.
    data : array like
        The 2D image (RGB array) to save.
    ext : {'png', 'jpeg', 'tiff'}, optional
        File extension, defaults to "png".

    Examples
    --------
    >>> import numpy as np
    >>> from plantdb.commons.io import write_image
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file("test_image")
    >>> rng = np.random.default_rng()
    >>> img = np.array(rng.random((5, 5, 3))*255, dtype='uint8')  # an 8bit 5x5 RGB image
    >>> write_image(f, img)
    """
    _writer(file, data, ext, _write_image, **kwargs)
    return

write_json

write_json(file, data, ext='json', **kwargs)

Writes a JSON to a ROMI database file or to a given path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	If a File instance, the file will be saved to the associated database/scan/fileset. Else, write the data to the given file path, ignoring the extension parameter ext.	required
data	dict	The dictionary to save as a JSON file.	required
ext	str	File extension, defaults to "json".	'json'

Examples:

>>> from plantdb.commons.io import write_json
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file("test_json")
>>> data = {"test": False, 'ROMI': 'RObotics for MIcrofarms'}
>>> write_json(f, data)

Source code in plantdb/commons/io.py

def write_json(file, data, ext="json", **kwargs):
    """Writes a JSON to a ROMI database file or to a given path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        If a ``File`` instance, the file will be saved to the associated database/scan/fileset.
        Else, write the `data` to the given file path, ignoring the extension parameter `ext`.
    data : dict
        The dictionary to save as a JSON file.
    ext : str, optional
        File extension, defaults to "json".

    Examples
    --------
    >>> from plantdb.commons.io import write_json
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file("test_json")
    >>> data = {"test": False, 'ROMI': 'RObotics for MIcrofarms'}
    >>> write_json(f, data)
    """
    _writer(file, data, ext, _write_json, **kwargs)
    return

write_npz

write_npz(file, data, **kwargs)

Writes a dictionary of arrays to a ROMI database file or to a given path.

Parameters:

Name	Type	Description	Default
dbfile	File or Path or str	If a File instance, the file will be saved to the associated database/scan/fileset. Else, write the data to the given file path, ignoring the extension parameter ext.	required
data	dict of numpy.ndarray	A dictionary of arrays to save as a single compressed '.npz' file.	required

Examples:

>>> import numpy as np
>>> from plantdb.commons.io import read_npz, write_npz
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file('test_npz')
>>> rng = np.random.default_rng()
>>> npz = {f"{i}": rng.random((10, 10, 3)) for i in range(5)}
>>> write_npz(f, npz)

Source code in plantdb/commons/io.py

def write_npz(file, data, **kwargs):
    """Writes a dictionary of arrays to a ROMI database file or to a given path.

    Parameters
    ----------
    dbfile : plantdb.commons.db.File or pathlib.Path or str
        If a ``File`` instance, the file will be saved to the associated database/scan/fileset.
        Else, write the `data` to the given file path, ignoring the extension parameter `ext`.
    data : dict of numpy.ndarray
        A dictionary of arrays to save as a single compressed '.npz' file.

    Examples
    --------
    >>> import numpy as np
    >>> from plantdb.commons.io import read_npz, write_npz
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file('test_npz')
    >>> rng = np.random.default_rng()
    >>> npz = {f"{i}": rng.random((10, 10, 3)) for i in range(5)}
    >>> write_npz(f, npz)
    """
    _writer(file, data, 'npz', _write_npz, **kwargs)
    return

write_point_cloud

write_point_cloud(file, data, ext='ply', **kwargs)

Writes a point cloud to a ROMI database file or to a given path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	If a File instance, the file will be saved to the associated database/scan/fileset. Else, write the data to the given file path, ignoring the extension parameter ext.	required
data	PointCloud	The point cloud object to save.	required
ext	str	File extension, defaults to "ply".	'ply'

Examples:

>>> import open3d as o3d
>>> import numpy as np
>>> from plantdb.commons.io import write_point_cloud
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file('test_npz')
>>> pcd = o3d.geometry.PointCloud()
>>> pcd.points = o3d.utility.Vector3dVector(np.array([[1, 2, 3]]))
>>> write_point_cloud(f,pcd)

Source code in plantdb/commons/io.py

def write_point_cloud(file, data, ext="ply", **kwargs):
    """Writes a point cloud to a ROMI database file or to a given path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        If a ``File`` instance, the file will be saved to the associated database/scan/fileset.
        Else, write the `data` to the given file path, ignoring the extension parameter `ext`.
    data : open3d.geometry.PointCloud
        The point cloud object to save.
    ext : str, optional
        File extension, defaults to "ply".

    Examples
    --------
    >>> import open3d as o3d
    >>> import numpy as np
    >>> from plantdb.commons.io import write_point_cloud
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file('test_npz')
    >>> pcd = o3d.geometry.PointCloud()
    >>> pcd.points = o3d.utility.Vector3dVector(np.array([[1, 2, 3]]))
    >>> write_point_cloud(f,pcd)
    """
    _writer(file, data, ext, _write_point_cloud, **kwargs)
    return

write_toml

write_toml(file, data, ext='toml', **kwargs)

Writes a TOML to a ROMI database file or to a given path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	If a File instance, the file will be saved to the associated database/scan/fileset. Else, write the data to the given file path, ignoring the extension parameter ext.	required
data	dict	The dictionary to save as a TOML file.	required
ext	str	File extension, defaults to "toml".	'toml'

Examples:

>>> from plantdb.commons.io import write_toml
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> f = fs.create_file("test_json")
>>> data = {"test": True, 'ROMI': 'RObotics for MIcrofarms'}
>>> write_toml(f, data)

Source code in plantdb/commons/io.py

def write_toml(file, data, ext="toml", **kwargs):
    """Writes a TOML to a ROMI database file or to a given path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        If a ``File`` instance, the file will be saved to the associated database/scan/fileset.
        Else, write the `data` to the given file path, ignoring the extension parameter `ext`.
    data : dict
        The dictionary to save as a TOML file.
    ext : str, optional
        File extension, defaults to "toml".

    Examples
    --------
    >>> from plantdb.commons.io import write_toml
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> f = fs.create_file("test_json")
    >>> data = {"test": True, 'ROMI': 'RObotics for MIcrofarms'}
    >>> write_toml(f, data)
    """
    _writer(file, data, ext, _write_toml, **kwargs)
    return

write_torch

write_torch(file, data, ext='pt', **kwargs)

Writes a torch tensor to a ROMI database file or to a given path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	If a File instance, the file will be saved to the associated database/scan/fileset. Else, write the data to the given file path, ignoring the extension parameter ext.	required
data	TorchTensor	The torch tensor object to save.	required
ext	str	File extension, defaults to "pt".	'pt'

Source code in plantdb/commons/io.py

def write_torch(file, data, ext="pt", **kwargs):
    """Writes a torch tensor to a ROMI database file or to a given path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        If a ``File`` instance, the file will be saved to the associated database/scan/fileset.
        Else, write the `data` to the given file path, ignoring the extension parameter `ext`.
    data : TorchTensor
        The torch tensor object to save.
    ext : str, optional
        File extension, defaults to "pt".
    """
    _writer(file, data, ext, _write_torch, **kwargs)
    return

write_triangle_mesh

write_triangle_mesh(file, data, ext='ply', **kwargs)

Writes a triangular mesh to a ROMI database file or to a given path.

Parameters:

Name	Type	Description	Default
file	File or Path or str	If a File instance, the file will be saved to the associated database/scan/fileset. Else, write the data to the given file path, ignoring the extension parameter ext.	required
data	TriangleMesh	The triangular mesh object to save.	required
ext	str	File extension, defaults to "ply".	'ply'

Source code in plantdb/commons/io.py

def write_triangle_mesh(file, data, ext="ply", **kwargs):
    """Writes a triangular mesh to a ROMI database file or to a given path.

    Parameters
    ----------
    file : plantdb.commons.db.File or pathlib.Path or str
        If a ``File`` instance, the file will be saved to the associated database/scan/fileset.
        Else, write the `data` to the given file path, ignoring the extension parameter `ext`.
    data : open3d.geometry.TriangleMesh
        The triangular mesh object to save.
    ext : str, optional
        File extension, defaults to "ply".
    """
    _writer(file, data, ext, _write_triangle_mesh, **kwargs)
    return

write_volume

write_volume(file, data, ext='tiff', **kwargs)

Writes a volume image to a ROMI database file.

Parameters:

Name	Type	Description	Default
file	File	The File object used to write the associated file.	required
data	array like	The 3D array to save as volume image.	required
ext	str	File extension, defaults to "tiff".	'tiff'

Other Parameters:

Name	Type	Description
compress	bool	Indicate if the volume file should be compressed. Defaults to True.

Examples:

>>> import numpy as np
>>> from plantdb.commons.fsdb import FSDB
>>> from plantdb.commons.io import write_volume
>>> from plantdb.commons.fsdb import Scan, Fileset, File
>>> from plantdb.commons.fsdb import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> db.connect()
>>> scan = db.get_scan("myscan_001")
>>> fs = scan.get_fileset("fileset_001")
>>> vol = np.ones((50, 10, 10))  # stupid volume file with only `1` values
>>> f_lzw = fs.create_file('test_volume_compress')
>>> write_volume(f_lzw, vol)
>>> f = fs.create_file('test_volume')
>>> write_volume(f, vol, compress=False)
>>> print(f_lzw.path().stat().st_size)
15283
>>> print(f.path().stat().st_size)
48994

Source code in plantdb/commons/io.py

def write_volume(file, data, ext="tiff", **kwargs):
    """Writes a volume image to a ROMI database file.

    Parameters
    ----------
    file : plantdb.commons.db.File
        The `File` object used to write the associated file.
    data : array like
        The 3D array to save as volume image.
    ext : str, optional
        File extension, defaults to "tiff".

    Other Parameters
    ----------------
    compress : bool, optional
        Indicate if the volume file should be compressed.
        Defaults to ``True``.

    Examples
    --------
    >>> import numpy as np
    >>> from plantdb.commons.fsdb import FSDB
    >>> from plantdb.commons.io import write_volume
    >>> from plantdb.commons.fsdb import Scan, Fileset, File
    >>> from plantdb.commons.fsdb import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> db.connect()
    >>> scan = db.get_scan("myscan_001")
    >>> fs = scan.get_fileset("fileset_001")
    >>> vol = np.ones((50, 10, 10))  # stupid volume file with only `1` values
    >>> f_lzw = fs.create_file('test_volume_compress')
    >>> write_volume(f_lzw, vol)
    >>> f = fs.create_file('test_volume')
    >>> write_volume(f, vol, compress=False)
    >>> print(f_lzw.path().stat().st_size)
    15283
    >>> print(f.path().stat().st_size)
    48994
    """
    _writer(file, data, ext, _write_volume, **kwargs)
    return

write_voxel_grid

write_voxel_grid(file, data, ext='ply', **kwargs)

Writes a voxel grid to a ROMI database file.

Parameters:

Name	Type	Description	Default
file	File	The File object used to write the associated file.	required
data	VoxelGrid	The voxel grid object to save.	required
ext	str	File extension, defaults to "ply".	'ply'

See Also

plantdb.commons.io._write_voxel_grid open3d.cuda.pybind.io.write_voxel_grid

Source code in plantdb/commons/io.py

def write_voxel_grid(file, data, ext="ply", **kwargs):
    """Writes a voxel grid to a ROMI database file.

    Parameters
    ----------
    file : plantdb.commons.db.File
        The `File` object used to write the associated file.
    data : open3d.geometry.VoxelGrid
        The voxel grid object to save.
    ext : str, optional
        File extension, defaults to "ply".

    See Also
    --------
    plantdb.commons.io._write_voxel_grid
    open3d.cuda.pybind.io.write_voxel_grid
    """
    _writer(file, data, ext, _write_voxel_grid, **kwargs)
    return