hdfmap 0.4__py3-none-any.whl

hdfmap/logging.py

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+"""
+Create logging objects and functions
+
+See https://docs.python.org/3/howto/logging.html
+"""
+
+import logging
+
+# Setup config - doesn't work properly without this
+logging.basicConfig()   # setup logging
+
+
+def create_logger(name: str) -> logging.Logger:
+    """Create new logger instance"""
+    return logging.getLogger(name)
+
+
+def set_all_logging_level(level: str | int):
+    """
+    Set logging level of all loggers
+    Logging Levels (see builtin module logging)
+        'notset'   |  0
+        'debug'    |  10
+        'info'     |  20
+        'warning'  |  30
+        'error'    |  40
+        'critical' |  50
+    :param level: str level name or int level
+    :return: None
+    """
+    try:
+        level = level.upper()
+        level = logging.getLevelNamesMapping()[level]
+    except AttributeError:
+        level = int(level)
+
+    logging_logger = logging.getLogger(__name__)
+    for logger in [logging.getLogger(name) for name in logging.root.manager.loggerDict]:
+        logger.setLevel(level)
+    logging_logger.info(f"Logging level set to {level}")

hdfmap/nexus.py

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+"""
+Nexus Related functions and nexus class
+"""
+
+import h5py
+
+from .logging import create_logger
+from .hdfmap_class import HdfMap, build_hdf_path, generate_identifier, disp_dict
+
+NX_CLASS = 'NX_class'
+NX_ENTRY = 'NXentry'
+NX_DATA = 'NXdata'
+NX_LOCALNAME = 'local_name'
+NX_DEFAULT = 'default'
+NX_MEASUREMENT = 'measurement'
+NX_SCANFIELDS = 'scan_fields'
+NX_SIGNAL = 'signal'
+NX_AXES = 'axes'
+NX_DETECTOR = 'NXdetector'
+NX_DETECTOR_DATA = 'data'
+logger = create_logger(__name__)
+
+
+def check_nexus_class(hdf_group: h5py.Group, nxclass: str) -> bool:
+    """
+    Check if hdf_group is a certain NX_class
+    :param hdf_group: hdf or nexus group object
+    :param nxclass: str name in NX_class attribute
+    :return: True/False
+    """
+    return (hdf_group and
+            (group_class := hdf_group.attrs.get(NX_CLASS)) is not None and
+            (group_class.decode() if isinstance(group_class, bytes) else group_class) == nxclass)
+
+
+def default_nxentry(hdf_file: h5py.File) -> str | bytes:
+    """Return the default NXentry path, or the first NXentry if there is no default, errors if no NXentry"""
+    return entry if (
+            NX_DEFAULT in hdf_file.attrs and
+            isinstance(hdf_file.get(entry := hdf_file.attrs[NX_DEFAULT]), h5py.Group)
+    ) else next(path for path in hdf_file if check_nexus_class(hdf_file.get(path), NX_ENTRY))
+
+
+def default_nxdata(entry_group: h5py.Group) -> str | bytes:
+    """Return the default NXdata path within an NXentry group"""
+    nx_data_name = entry_group.attrs[NX_DEFAULT] if NX_DEFAULT in entry_group.attrs else NX_MEASUREMENT
+    if nx_data_name not in entry_group:
+        nx_data_name = next(name for name in entry_group if check_nexus_class(entry_group.get(name), NX_DATA))
+    return nx_data_name
+
+
+def find_nexus_data(hdf_file: h5py.File) -> tuple[list[str], str]:
+    """
+    Nexus compliant method of finding default plotting axes in hdf files
+     - find "default" entry group in top File group
+     - find "default" data group in entry (or 'measurement', or first 'NXdata')
+     - find "axes" attr in default data
+     - find "signal" attr in default data
+     - generate paths of signal and axes
+     if not nexus compliant, raises KeyError
+    This method is very fast but only works on nexus compliant files
+    :param hdf_file: open HDF file object, i.e. h5py.File(...)
+    :return axes_paths: list of str hdf paths for axes datasets
+    :return signal_path: str hdf path for signal dataset
+    """
+    # From: https://manual.nexusformat.org/examples/python/plotting/index.html
+    # find the default NXentry group
+    nx_entry_name = default_nxentry(hdf_file)
+    nx_entry = hdf_file[nx_entry_name]
+    # find the default NXdata group
+    nx_data_name = default_nxdata(nx_entry)
+    nx_data = nx_entry[nx_data_name]
+    # find the axes field(s)
+    if isinstance(axes := nx_data.attrs[NX_AXES], (str, bytes)):
+        axes_paths = [build_hdf_path(nx_entry_name, nx_data_name, axes)]
+    else:
+        axes_paths = [build_hdf_path(nx_entry_name, nx_data_name, _axes) for _axes in axes]
+    # get the signal field
+    if NX_SIGNAL in nx_data.attrs:
+        signal_path = build_hdf_path(nx_entry_name, nx_data_name, nx_data.attrs[NX_SIGNAL])
+    else:
+        signal_path = build_hdf_path(nx_entry_name, nx_data_name, NX_DETECTOR_DATA)
+    return axes_paths, signal_path
+
+
+def find_nexus_data_strict(hdf_file: h5py.File) -> tuple[list[h5py.Dataset], h5py.Dataset]:
+    """
+    Nexus compliant method of finding default plotting axes in hdf files
+     - find "default" entry group in top File group
+     - find "default" data group in entry
+     - find "axes" attr in default data
+     - find "signal" attr in default data
+     - generate paths of signal and axes
+     if not nexus compliant, raises KeyError
+    This method is very fast but only works on nexus compliant files
+    :param hdf_file: open HDF file object, i.e. h5py.File(...)
+    :return axes_datasets: list of dataset objects for axes
+    :return signal_dataset: dataset object for plot axis
+    """
+    # From: https://manual.nexusformat.org/examples/python/plotting/index.html
+    # find the default NXentry group
+    nx_entry = hdf_file[hdf_file.attrs[NX_DEFAULT]]
+    # find the default NXdata group
+    nx_data = nx_entry[nx_entry.attrs[NX_DEFAULT]]
+    # find the axes field(s)
+    if isinstance(nx_data.attrs[NX_AXES], (str, bytes)):
+        axes_datasets = [nx_data[nx_data.attrs[NX_AXES]]]
+    else:
+        axes_datasets = [nx_data[_axes] for _axes in nx_data.attrs[NX_AXES]]
+    # find the signal field
+    signal_dataset = nx_data[nx_data.attrs[NX_SIGNAL]]
+    return axes_datasets, signal_dataset
+
+
+class NexusMap(HdfMap):
+    """
+    HdfMap for Nexus (.nxs) files
+
+    Extends the HdfMap class with additional behaviours for NeXus files.
+    http://www.nexusformat.org/
+
+    E.G.
+    nxmap = NexusMap()
+    with h5py.File('file.nxs', 'r') as nxs:
+        nxmap.populate(nxs, default_entry_only=True)  # populates only from the default entry
+
+    # Special behaviour
+    nxmap['axes'] -> return path of default axes dataset
+    nxmap['signal'] -> return path of default signal dataset
+    """
+
+    def __repr__(self):
+        return f"NexusMap based on '{self.filename}'"
+
+    def all_nxclasses(self) -> list[str]:
+        """Return list of unique NX_class attributes used in NXgroups"""
+        return list({
+            nxclass.decode() if isinstance(nxclass, bytes) else nxclass
+            for path, grp in self.groups.items() if (nxclass := grp.attrs.get(NX_CLASS))
+        })
+
+    def info_nexus(self) -> str:
+        """Return str info on nexus format"""
+        out = f"{repr(self)}\n"
+        out += f"{NX_CLASS}:\n"
+        nx_classes = self.all_nxclasses()
+        out += disp_dict({k: v for k, v in self.classes.items() if k in nx_classes}, 20)
+        out += '\nDefaults:\n'
+        out += f"  @{NX_DEFAULT}: {self.find_attr(NX_DEFAULT)}\n"
+        out += f"  @{NX_AXES}: {self.find_attr(NX_AXES)}\n"
+        out += f"  @{NX_SIGNAL}: {self.find_attr(NX_SIGNAL)}\n"
+        return out
+
+    def _default_nexus_paths(self, hdf_file):
+        """Load Nexus default axes and signal"""
+        try:
+            axes_paths, signal_path = find_nexus_data(hdf_file)
+            # TODO: add method of including multiple axes, e.g. axes1, axes2, ..., or self.get_axes
+            if axes_paths and axes_paths[0] in hdf_file:
+                self.arrays[NX_AXES] = axes_paths[0]
+                logger.info(f"DEFAULT axes: {axes_paths}")
+            if signal_path in hdf_file:
+                self.arrays[NX_SIGNAL] = signal_path
+                logger.info(f"DEFAULT signal: {signal_path}")
+        except KeyError:
+            pass
+
+    def _scannables_from_scan_fields_or_nxdata(self, hdf_file: h5py.File):
+        """Generate scannables from scan_field names or default NXdata"""
+        # find 'scan_fields' to generate scannables list
+        if NX_SCANFIELDS in self.arrays:
+            scan_fields_path = self.arrays[NX_SCANFIELDS]
+            scan_fields = hdf_file[scan_fields_path][()]
+            logger.info(f"NX ScanFields: {scan_fields_path}: {scan_fields}")
+            self.generate_scannables_from_names(scan_fields)
+        else:
+            # find the default NXdata group and generate the scannables list
+            nx_entry = hdf_file.get(default_nxentry(hdf_file))
+            nx_data = nx_entry.get(default_nxdata(nx_entry))
+            logger.info(f"{nx_entry}, {nx_data}")
+            if nx_data:
+                logger.info(f"NX Data: {nx_data.name}")
+                self.generate_scannables_from_group(nx_data)
+
+        if not self.scannables:
+            logger.warning("No NXdata found, scannables not populated!")
+
+    def _image_data_from_nxdetector(self):
+        """find the NXdetector group and assign the image data"""
+        self.image_data = {}
+        if NX_DETECTOR in self.classes:
+            for group_path in self.classes[NX_DETECTOR]:
+                detector_name = generate_identifier(group_path)
+                data_path = build_hdf_path(group_path, NX_DETECTOR_DATA)
+                if data_path in self.datasets and len(self.datasets[data_path].shape) > 1:
+                    self.image_data[detector_name] = data_path
+
+        if not self.image_data:
+            logger.warning("!!!Warning: No NXdetector found, image_data not populated!")
+
+    def populate(self, hdf_file: h5py.File, groups=None, default_entry_only=False):
+        """
+        Populate only datasets from default or first entry, with scannables from given groups.
+        Automatically load defaults (axes, signal) and generate scannables from default group
+        :param hdf_file: HDF File object
+        :param groups: list of group names or NXClass names to search for datasets, within default entry
+        :param default_entry_only: if True, only the first or default entry will be loaded
+        """
+        self.filename = hdf_file.filename
+
+        # Add defaults to arrays
+        self._default_nexus_paths(hdf_file)
+
+        if default_entry_only:
+            entries = [default_nxentry(hdf_file)]
+        else:
+            entries = [entry for entry in hdf_file if check_nexus_class(hdf_file.get(entry), NX_ENTRY)]
+
+        for entry in entries:
+            # find default or first entry
+            nx_entry = hdf_file.get(entry)
+            if nx_entry is None:
+                logger.warning(
+                    f"NX Entry {entry} doesn't exist - may be a missing link.\n" +
+                    f"Missing link: {hdf_file.get(entry, getlink=True)}"
+                )
+                continue  # group may be missing due to a broken link
+            hdf_path = build_hdf_path(entry)
+            logger.debug(f"NX Entry: {hdf_path}")
+            self.all_paths.append(hdf_path)
+            self._store_group(nx_entry, hdf_path, entry)
+            self._populate(nx_entry, root=hdf_path, groups=groups)  # nx_entry.name can be wrong!
+
+        if not self.datasets:
+            logger.warning("!!!Warning: No datasets found!")
+
+        self._scannables_from_scan_fields_or_nxdata(hdf_file)
+
+        # find the NXdetector group and assign the image data
+        self._image_data_from_nxdetector()

hdfmap/reloader_class.py

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+"""
+Reloader class
+"""
+
+import h5py
+import numpy as np
+
+from .hdfmap_class import HdfMap
+from .nexus import NexusMap
+from .file_functions import load_hdf, create_hdf_map, create_nexus_map
+
+
+class HdfLoader:
+    """
+    HDF Loader
+    contains the filename and hdfmap for a HDF file, the hdfmap contains all the dataset paths and a
+    namespace, allowing data to be called from the file using variable names, loading only the required datasets
+    for each operation.
+    E.G.
+        hdf = HdfLoader('file.hdf')
+        [data1, data2] = hdf.get_data(['dataset_name_1', 'dataset_name_2'])
+        data = hdf.eval('dataset_name_1 * 100 + 2')
+        string = hdf.format('my data is {dataset_name_1:.2f}')
+    """
+
+    def __init__(self, hdf_filename: str, hdf_map: HdfMap | None = None):
+        self.filename = hdf_filename
+        if hdf_map is None:
+            self.map = create_hdf_map(hdf_filename)
+        else:
+            self.map = hdf_map
+
+    def __repr__(self):
+        return f"HdfReloader('{self.filename}')"
+
+    def __str__(self):
+        with self._load() as hdf:
+            out = self.map.info_data(hdf)
+        return out
+
+    def __getitem__(self, item):
+        return self.get_data(item)
+
+    def __call__(self, expression):
+        return self.eval(expression)
+
+    def _load(self) -> h5py.File:
+        return load_hdf(self.filename)
+
+    def get_hdf_path(self, name_or_path: str) -> str or None:
+        """Return hdf path of object in HdfMap"""
+        return self.map.get_path(name_or_path)
+
+    def find_hdf_paths(self, string: str, name_only: bool = True) -> list[str]:
+        """
+        Find any dataset paths that contain the given string argument
+        :param string: str to find in list of datasets
+        :param name_only: if True, search only the name of the dataset, not the full path
+        :return: list of hdf paths
+        """
+        return self.map.find_paths(string, name_only)
+
+    def find_names(self, string: str) -> list[str]:
+        """
+        Find any dataset names that contain the given string argument, searching names in self.combined
+        :param string: str to find in list of datasets
+        :return: list of names
+        """
+        return self.map.find_names(string)
+
+    def get_data(self, *name_or_path, index: slice = (), default=None, direct_load=False):
+        """
+        Return data from dataset in file, converted into either datetime, str or squeezed numpy.array objects
+        See hdfmap.eval_functions.dataset2data for more information.
+        :param name_or_path: str name or path pointing to dataset in hdf file
+        :param index: index or slice of data in hdf file
+        :param default: value to return if name not found in hdf file
+        :param direct_load: return str, datetime or squeezed array if False, otherwise load data directly
+        :return: dataset2data(dataset) -> datetime, str or squeezed array as required.
+        """
+        with self._load() as hdf:
+            out = [self.map.get_data(hdf, name, index, default, direct_load) for name in name_or_path]
+        if len(name_or_path) == 1:
+            return out[0]
+        return out
+
+    def get_image(self, index: slice = None) -> np.ndarray:
+        """
+        Get image data from file, using default image path
+        :param index: (slice,) or None to take the middle image
+        :return: numpy array of image
+        """
+        with self._load() as hdf:
+            return self.map.get_image(hdf, index)
+
+    def get_metadata(self, defaults=None):
+        with self._load() as hdf:
+            return self.map.get_metadata(hdf, default=defaults)
+
+    def get_scannables(self):
+        """Return scannables from file (values associated with hdfmap.scannables)"""
+        with self._load() as hdf:
+            return self.map.get_scannables(hdf)
+
+    def eval(self, expression: str):
+        """
+        Evaluate an expression using the namespace of the hdf file
+        :param expression: str expression to be evaluated
+        :return: eval(expression)
+        """
+        with self._load() as hdf:
+            return self.map.eval(hdf, expression)
+
+    def format(self, expression: str):
+        """
+        Evaluate a formatted string expression using the namespace of the hdf file
+        :param expression: str expression using {name} format specifiers
+        :return: eval_hdf(f"expression")
+        """
+        with self._load() as hdf:
+            return self.map.format_hdf(hdf, expression)
+
+
+class NexusLoader(HdfLoader):
+    """
+    Nexus Loader
+    contains the filename and hdfmap for a NeXus file, the hdfmap contains all the dataset paths and a
+    namespace, allowing data to be called from the file using variable names, loading only the required datasets
+    for each operation.
+    E.G.
+        hdf = NexusLoader('file.hdf')
+        [data1, data2] = hdf.get_data(['dataset_name_1', 'dataset_name_2'])
+        data = hdf.eval('dataset_name_1 * 100 + 2')
+        string = hdf.format('my data is {dataset_name_1:.2f}')
+    """
+
+    def __init__(self, nxs_filename: str, hdf_map: NexusMap | None = None):
+        if not hdf_map:
+            hdf_map = create_nexus_map(nxs_filename)
+        super().__init__(nxs_filename, hdf_map)

hdfmap-0.4.dist-info/LICENSE

@@ -0,0 +1,201 @@
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