pymodaq_data 0.0.1__py3-none-any.whl

pymodaq_data/h5modules/browsing.py

@@ -0,0 +1,101 @@
+# -*- coding: utf-8 -*-
+"""
+Created the 15/11/2022
+
+@author: Sebastien Weber
+"""
+from typing import Tuple
+import os
+from collections import OrderedDict
+from typing import List
+import warnings
+import logging
+import webbrowser
+import numpy as np
+from pathlib import Path
+from packaging import version as version_mod
+
+from pymodaq_utils.logger import set_logger, get_module_name
+from pymodaq_utils.config import Config
+from .backends import H5Backend
+from .exporter import ExporterFactory
+
+config = Config()
+logger = set_logger(get_module_name(__file__))
+
+
+class H5BrowserUtil(H5Backend):
+    """Utility object to interact and get info and data from a hdf5 file
+
+    Inherits H5Backend and all its functionalities
+
+    Parameters
+    ----------
+    backend: str
+        The used hdf5 backend: either tables, h5py or h5pyd
+    """
+    def __init__(self, backend='tables'):
+        super().__init__(backend=backend)
+
+    def export_data(self, node_path='/', filesavename: str = 'datafile.h5', filter=None):
+        """Initialize the correct exporter and export the node"""
+
+        # Format the node and file type
+        filepath = Path(filesavename)
+        node = self.get_node(node_path)
+        # Separate dot from extension
+        extension = filepath.suffix[1:]
+        # Obtain the suitable exporter object
+        exporter = ExporterFactory.create_exporter(
+            extension,
+            ExporterFactory.get_format_from_filter(filter))
+        # Export the data
+        exporter.export_data(node, filepath)
+
+    def get_h5file_scans(self, where='/'):
+        """Get the list of the scan nodes in the file
+
+        Parameters
+        ----------
+        where: str
+            the path in the file
+
+        Returns
+        -------
+        list of dict
+            dict with keys: scan_name, path (within the file) and data (the live scan png image)
+        """
+        # TODO add a test for this method
+        scan_list = []
+        where = self.get_node(where)
+        for node in self.walk_nodes(where):
+            if 'pixmap2D' in node.attrs:
+                scan_list.append(
+                    dict(scan_name='{:s}_{:s}'.format(node.parent_node.name, node.name), path=node.path,
+                         data=node.attrs['pixmap2D']))
+
+        return scan_list
+
+    def get_h5_attributes(self, node_path):
+        """
+        """
+        node = self.get_node(node_path)
+        attrs_names = node.attrs.attrs_name
+        attr_dict = OrderedDict(node.attrs.to_dict())
+
+        settings = None
+        scan_settings = None
+        if 'settings' in attrs_names:
+            if node.attrs['settings'] != '':
+                settings = node.attrs['settings']
+
+        if 'scan_settings' in attrs_names:
+            if node.attrs['scan_settings'] != '':
+                scan_settings = node.attrs['scan_settings']
+        pixmaps = []
+        for attr in attrs_names:
+            if 'pixmap' in attr:
+                pixmaps.append(node.attrs[attr])
+
+        return attr_dict, settings, scan_settings, pixmaps
+