utils

compute_fileset_matches

compute_fileset_matches(scan)

Return a dictionary mapping the scan tasks to fileset names.

Parameters:

Name	Type	Description	Default
scan	Scan	The scan instance to list the filesets from.	required

Returns:

Type	Description
dict	A dictionary mapping the scan tasks to fileset names.

Examples:

>>> from plantdb.server.core.utils import compute_fileset_matches
>>> from plantdb.commons.test_database import dummy_db
>>> db = dummy_db(with_fileset=True)
>>> scan = db.get_scan("myscan_001")
>>> compute_fileset_matches(scan)
{'fileset': 'fileset_001'}
>>> db.disconnect()  # clean up (delete) the temporary dummy database

Source code in plantdb/server/core/utils.py

def compute_fileset_matches(scan):
    """Return a dictionary mapping the scan tasks to fileset names.

    Parameters
    ----------
    scan : plantdb.commons.fsdb.core.Scan
        The scan instance to list the filesets from.

    Returns
    -------
    dict
        A dictionary mapping the scan tasks to fileset names.

    Examples
    --------
    >>> from plantdb.server.core.utils import compute_fileset_matches
    >>> from plantdb.commons.test_database import dummy_db
    >>> db = dummy_db(with_fileset=True)
    >>> scan = db.get_scan("myscan_001")
    >>> compute_fileset_matches(scan)
    {'fileset': 'fileset_001'}
    >>> db.disconnect()  # clean up (delete) the temporary dummy database
    """
    filesets_matches = {}
    for fs in scan.get_filesets():
        x = fs.id.split('_')[0]  # get the task name
        filesets_matches[x] = fs.id
    return filesets_matches

get_file_uri

get_file_uri(scan, fileset, file)

Return the URI for the corresponding scan/fileset/file tree.

Parameters:

Name	Type	Description	Default
scan	Scan or str	A Scan instance or the name of the scan dataset.	required
fileset	Fileset or str	A Fileset instance or the name of the fileset.	required
file	File or str	A File instance or the name of the file.	required

Returns:

Type	Description
str	The URI for the corresponding scan/fileset/file tree.

Examples:

>>> from plantdb.server.core.utils import compute_fileset_matches
>>> from plantdb.server.core.utils import get_file_uri
>>> from plantdb.commons.test_database import test_database
>>> db = test_database('real_plant_analyzed')
>>> db.connect()
>>> scan = db.get_scan('real_plant_analyzed')
>>> fs_match = compute_fileset_matches(scan)
>>> fs = scan.get_fileset(fs_match['PointCloud'])
>>> f = fs.get_file("PointCloud")
>>> get_file_uri(scan, fs, f)
'/files/real_plant_analyzed/PointCloud_1_0_1_0_10_0_7ee836e5a9/PointCloud.ply'

Source code in plantdb/server/core/utils.py

def get_file_uri(scan, fileset, file):
    """Return the URI for the corresponding `scan/fileset/file` tree.

    Parameters
    ----------
    scan : plantdb.commons.fsdb.core.Scan or str
        A ``Scan`` instance or the name of the scan dataset.
    fileset : plantdb.commons.fsdb.core.Fileset or str
        A ``Fileset`` instance or the name of the fileset.
    file : plantdb.commons.fsdb.core.File or str
        A ``File`` instance or the name of the file.

    Returns
    -------
    str
        The URI for the corresponding `scan/fileset/file` tree.

    Examples
    --------
    >>> from plantdb.server.core.utils import compute_fileset_matches
    >>> from plantdb.server.core.utils import get_file_uri
    >>> from plantdb.commons.test_database import test_database
    >>> db = test_database('real_plant_analyzed')
    >>> db.connect()
    >>> scan = db.get_scan('real_plant_analyzed')
    >>> fs_match = compute_fileset_matches(scan)
    >>> fs = scan.get_fileset(fs_match['PointCloud'])
    >>> f = fs.get_file("PointCloud")
    >>> get_file_uri(scan, fs, f)
    '/files/real_plant_analyzed/PointCloud_1_0_1_0_10_0_7ee836e5a9/PointCloud.ply'
    """
    from plantdb.commons.fsdb.core import Scan
    from plantdb.commons.fsdb.core import Fileset
    from plantdb.commons.fsdb.core import File
    scan_id = scan.id if isinstance(scan, Scan) else scan
    fileset_id = fileset.id if isinstance(fileset, Fileset) else fileset
    file_id = file.path().name if isinstance(file, File) else file
    return f"/files/{scan_id}/{fileset_id}/{file_id}"

get_image_uri

get_image_uri(scan, fileset, file, size='orig', as_base64=False)

Return the URI for the corresponding scan/fileset/file tree.

Parameters:

Name	Type	Description	Default
scan	Scan or str	A Scan instance or the name of the scan dataset.	required
fileset	Fileset or str	A Fileset instance or the name of the fileset.	required
file	File or str	A File instance or the name of the file.	required
size	(orig, large, thumb)	If an integer, use it as the size of the cached image to create and return. Otherwise, should be one of the following strings, default to 'orig': 'thumb': image max width and height to 150. 'large': image max width and height to 1500; 'orig': original image, no chache;	'orig'
as_base64	bool	A boolean flag indicating whether to return an image as a base64 string.	False

Returns:

Type	Description
str	The URI for the corresponding scan/fileset/file tree.

Examples:

>>> from plantdb.server.core.utils import get_image_uri
>>> from plantdb.commons.test_database import test_database
>>> from plantdb.server.core.utils import compute_fileset_matches
>>> db = test_database('real_plant_analyzed')
>>> db.connect()
>>> scan = db.get_scan('real_plant_analyzed')
>>> get_image_uri(scan, 'images', '00000_rgb.jpg', size='orig')
'/image/real_plant_analyzed/images/00000_rgb.jpg?size=orig'
>>> get_image_uri(scan, 'images', '00011_rgb.jpg', size='thumb', as_base64=True)
'/image/real_plant_analyzed/images/00011_rgb.jpg?size=thumb&as_base64=true'

Source code in plantdb/server/core/utils.py

def get_image_uri(scan, fileset, file, size="orig", as_base64=False):
    """Return the URI for the corresponding `scan/fileset/file` tree.

    Parameters
    ----------
    scan : plantdb.commons.fsdb.core.Scan or str
        A ``Scan`` instance or the name of the scan dataset.
    fileset : plantdb.commons.fsdb.core.Fileset or str
        A ``Fileset`` instance or the name of the fileset.
    file : plantdb.commons.fsdb.core.File or str
        A ``File`` instance or the name of the file.
    size : {'orig', 'large', 'thumb'} or int, optional
        If an integer, use it as the size of the cached image to create and return.
        Otherwise, should be one of the following strings, default to `'orig'`:

          - `'thumb'`: image max width and height to `150`.
          - `'large'`: image max width and height to `1500`;
          - `'orig'`: original image, no chache;
    as_base64 : bool, optional
        A boolean flag indicating whether to return an image as a base64 string.

    Returns
    -------
    str
        The URI for the corresponding `scan/fileset/file` tree.

    Examples
    --------
    >>> from plantdb.server.core.utils import get_image_uri
    >>> from plantdb.commons.test_database import test_database
    >>> from plantdb.server.core.utils import compute_fileset_matches
    >>> db = test_database('real_plant_analyzed')
    >>> db.connect()
    >>> scan = db.get_scan('real_plant_analyzed')
    >>> get_image_uri(scan, 'images', '00000_rgb.jpg', size='orig')
    '/image/real_plant_analyzed/images/00000_rgb.jpg?size=orig'
    >>> get_image_uri(scan, 'images', '00011_rgb.jpg', size='thumb', as_base64=True)
    '/image/real_plant_analyzed/images/00011_rgb.jpg?size=thumb&as_base64=true'
    """
    from plantdb.commons.fsdb.core import Scan
    from plantdb.commons.fsdb.core import Fileset
    from plantdb.commons.fsdb.core import File
    scan_id = scan.id if isinstance(scan, Scan) else scan
    fileset_id = fileset.id if isinstance(fileset, Fileset) else fileset
    file_id = file.path().name if isinstance(file, File) else file

    # Assemble optional query parameters
    query: dict[str, str] = {}
    if size is not None:
        query["size"] = str(size)
    if as_base64:
        # Use lower‑case JSON‑style booleans for consistency
        query["as_base64"] = str(as_base64).lower()

    query_str = f"?{parse.urlencode(query)}" if query else ""
    return f"/image/{scan_id}/{fileset_id}/{file_id}{query_str}"

get_scan_date

get_scan_date(scan)

Get the acquisition datetime of a scan.

Try to get the data from the scan metadata 'acquisition_date', else from the directory creation time.

Parameters:

Name	Type	Description	Default
scan	Scan	The scan instance to get the date & time from.	required

Returns:

Type	Description
str	The formatted datetime string.

Examples:

>>> from plantdb.server.core.utils import get_scan_date
>>> from plantdb.commons.test_database import test_database
>>> db = test_database(['real_plant_analyzed', 'virtual_plant_analyzed'])
>>> db.connect()
>>> scan = db.get_scan('real_plant_analyzed')
>>> print(get_scan_date(scan))
>>> scan = db.get_scan('virtual_plant_analyzed')
>>> print(get_scan_date(scan))
>>> db.disconnect()

Source code in plantdb/server/core/utils.py

def get_scan_date(scan):
    """Get the acquisition datetime of a scan.

    Try to get the data from the scan metadata 'acquisition_date', else from the directory creation time.

    Parameters
    ----------
    scan : plantdb.commons.fsdb.core.Scan
        The scan instance to get the date & time from.

    Returns
    -------
    str
        The formatted datetime string.

    Examples
    --------
    >>> from plantdb.server.core.utils import get_scan_date
    >>> from plantdb.commons.test_database import test_database
    >>> db = test_database(['real_plant_analyzed', 'virtual_plant_analyzed'])
    >>> db.connect()
    >>> scan = db.get_scan('real_plant_analyzed')
    >>> print(get_scan_date(scan))
    >>> scan = db.get_scan('virtual_plant_analyzed')
    >>> print(get_scan_date(scan))
    >>> db.disconnect()
    """
    dt = scan.get_metadata('acquisition_date')
    try:
        assert isinstance(dt, str)
    except:
        # Get directory creation date as acquisition date
        c_time = scan.path().lstat().st_ctime
        dt = datetime.datetime.fromtimestamp(c_time)
        date = dt.strftime("%Y-%m-%d")
        time = dt.strftime("%H:%M:%S")
    else:
        date, time = dt.split(' ')
    return f"{date} {time}"

get_scan_template

get_scan_template(scan_id, error=False)

Template dictionary for a scan.

Source code in plantdb/server/core/utils.py

def get_scan_template(scan_id: str, error=False) -> dict:
    """Template dictionary for a scan."""
    return {
        "id": scan_id,
        "metadata": {
            "date": "01-01-00 00:00:00",
            "species": "N/A",
            "plant": "N/A",
            "environment": "N/A",
            "nbPhotos": 0,
            "files": {
                "metadata": None,
                "archive": None
            }
        },
        "thumbnailUri": "",
        "images": None,  # list of original image filenames
        "tasks_fileset": None,  # dict mapping task names to fileset names
        "filesUri": {},  # dict mapping task names to task file URI
        "isVirtual": False,
        "hasColmap": False,
        "hasPointCloud": False,
        "hasTriangleMesh": False,
        "hasCurveSkeleton": False,
        "hasTreeGraph": False,
        "hasAnglesAndInternodes": False,
        "hasAutomatedMeasures": False,
        "hasManualMeasures": False,
        "hasSegmentation2D": False,
        "hasPcdGroundTruth": False,
        "hasPointCloudEvaluation": False,
        "hasSegmentedPointCloud": False,
        "hasSegmentedPcdEvaluation": False,
        "error": error,
    }