pyTEMlib 0.2025.4.2__py3-none-any.whl → 0.2025.9.1__py3-none-any.whl

pyTEMlib/file_reader.py

@@ -0,0 +1,274 @@
+"""file_reader:  tools to load other data files
+
+##################################
+
+2025 copied from file_tools
+
+##################################
+"""
+import typing
+import collections
+import xml
+import numpy as np
+
+
+# =============================================
+#   Include  pycroscopy libraries                                      #
+# =============================================
+import pyNSID
+import sidpy
+
+def etree_to_dict(element: xml.etree.ElementTree.Element) -> dict[str, typing.Any]:
+    """Recursively converts an ElementTree object into a nested dictionary."""
+    d = {element.tag: {} if element.attrib else None}
+    children = list(element)
+    if children:
+        dd = collections.defaultdict(list)
+        for dc in map(etree_to_dict, children):
+            for k, v in dc.items():
+                dd[k].append(v)
+        d = {element.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
+    if element.attrib:
+        d[element.tag].update(('@' + k, v) for k, v in element.attrib.items())
+    if element.text:
+        text = element.text.strip()
+        if children or element.attrib:
+            if text:
+                d[element.tag]['#text'] = text
+        else:
+            d[element.tag] = text
+    return d
+
+def read_adorned_metadata(image: typing.Any) -> tuple[str, dict[str, typing.Any]]:
+    """Extract metadata from an adorned image."""
+    xml_str = image.metadata.metadata_as_xml
+    root = xml.etree.ElementTree.fromstring(xml_str)
+    metadata_dict = etree_to_dict(root)
+    detector = 'detector'
+
+    if 'Detectors' in metadata_dict['Metadata']:
+        if 'ScanningDetector' in metadata_dict['Metadata']['Detectors']:
+            detector = metadata_dict['Metadata']['Detectors']['ScanningDetector']['DetectorName']
+        elif 'ImagingDetector' in metadata_dict['Metadata']['Detectors']:
+            detector = metadata_dict['Metadata']['Detectors']['ImagingDetector']['DetectorName']
+    segment = ''
+    if 'CustomPropertyGroup' in  metadata_dict['Metadata']:
+        if 'CustomProperties' in metadata_dict['Metadata']['CustomPropertyGroup']:
+            for list_item in metadata_dict['Metadata']['CustomPropertyGroup']['CustomProperties']:
+                if isinstance(list_item, dict):
+                    for key in list_item:
+                        for item in list_item[key]:
+                            if '@name' in item:
+                                if item['@name']==  'DetectorCommercialName':
+                                    detector = item['@value']
+                                if item['@name']== 'StemSegment':
+                                    segment = '_'+item['@value']
+    return detector+segment, metadata_dict['Metadata']
+
+
+def get_metadata_from_adorned(ds: sidpy.Dataset):
+    """Extract relevant metadata from adorned image metadata and add to sidpy.Dataset"""
+    exp_meta = {}
+    orig_meta = ds.original_metadata
+    if 'Optics' in orig_meta:
+        if 'LastMeasuredScreenCurrent' in orig_meta['Optics']:
+            exp_meta['current'] = float(orig_meta['Optics']['LastMeasuredScreenCurrent'])
+        if 'ConvergenceAngle' in orig_meta['Optics']:
+            exp_meta['convergence_angle'] = float(orig_meta['Optics']['ConvergenceAngle'])
+        if 'AccelerationVoltage' in orig_meta['Optics']:
+            exp_meta['acceleration_voltage'] = float(orig_meta['Optics']['AccelerationVoltage'])
+        if 'SpotIndex' in orig_meta['Optics']:
+            exp_meta['spot_size'] = orig_meta['Optics']['SpotIndex']
+    if 'StagesSettings' in orig_meta:
+        if 'StagePosition' in orig_meta['StagesSettings']:
+            exp_meta['stage_position'] = orig_meta['StagesSettings']['StagePosition']
+    if 'Detectors' in orig_meta:
+        if 'ScanningDetector' in orig_meta['Detectors']:
+            exp_meta['detector'] = orig_meta['Detectors']['ScanningDetector']['DetectorName']
+        elif 'ImagingDetector' in orig_meta['Detectors']:
+            exp_meta['detector'] = orig_meta['Detectors']['ImagingDetector']['DetectorName']
+            exp_meta['exposure_time'] = orig_meta['Detectors']['ImagingDetector']['ExposureTime']
+    ds.metadata['experiment'] = exp_meta
+
+def adorned_to_sidpy(images: typing.Union[list[typing.Any], typing.Any]
+                     ) -> dict[str, sidpy.Dataset]:
+    """
+    Convert a list of adorned images to a dictionary of Sidpy datasets.
+    Each dataset is created from the image data and adorned metadata.       
+    The datasets are stored in a dictionary with keys 'Channel_000', 'Channel_001', etc.
+    The dimensions of the datasets are set based on the image data shape and pixel sizes.
+    The original metadata is also stored in the dataset.
+    Args:           
+        images (list or object): A list of adorned images or a single adorned image.
+        Returns:    
+        dict: A dictionary of Sidpy datasets, where each dataset corresponds to an image.
+    """
+
+    data_sets = {}
+    if not isinstance(images, list):
+        images = [images]
+    for index, image in enumerate(images):
+        name, original_metadata = read_adorned_metadata(image)
+        data_sets[f'Channel_{index:03}'] = sidpy.Dataset.from_array(image.data.T, title=name)
+        ds = data_sets[f'Channel_{index:03}']
+
+        ds.original_metadata = original_metadata
+
+        pixel_size_x_m = float(ds.original_metadata['BinaryResult']['PixelSize']['X']['#text'])
+        pixel_size_y_m = float(ds.original_metadata['BinaryResult']['PixelSize']['Y']['#text'])
+        pixel_size_x_nm = pixel_size_x_m * 1e9
+        pixel_size_y_nm = pixel_size_y_m * 1e9
+        if image.data.ndim == 3:
+            ds.data_type = 'image_stack'
+            ds.set_dimension(0, sidpy.Dimension(np.arange(image.data.shape[0]),
+                                           name='frame', units='frame', quantity='Length',
+                                           dimension_type='temporal'))
+            ds.set_dimension(1, sidpy.Dimension(np.arange(image.data.shape[1]) * pixel_size_y_nm,
+                                          name='y', units='nm', quantity='Length',
+                                          dimension_type='spatial'))
+            ds.set_dimension(2, sidpy.Dimension(np.arange(image.data.shape[2]) * pixel_size_x_nm,
+                                          name='x', units='nm', quantity='Length',
+                                          dimension_type='spatial'))
+        else:
+            ds.data_type = 'image'
+            ds.set_dimension(0, sidpy.Dimension(np.arange(image.data.shape[0]) * pixel_size_y_nm,
+                                          name='y', units='nm', quantity='Length',
+                                          dimension_type='spatial'))
+            ds.set_dimension(1, sidpy.Dimension(np.arange(image.data.shape[1]) * pixel_size_x_nm,
+                                          name='x', units='nm', quantity='Length',
+                                          dimension_type='spatial'))
+        get_metadata_from_adorned(ds)
+    return data_sets
+
+
+###############################################
+# Support old pyTEM file format
+###############################################
+
+def read_old_h5group(current_channel: typing.Any) -> typing.Optional[sidpy.Dataset]:
+    """Make a  sidpy.Dataset from pyUSID style hdf5 group
+
+    Parameters
+    ----------
+        current_channel: h5_group
+
+    Returns
+    -------
+        sidpy.Dataset
+    """
+
+    dim_dir = []
+    if 'nDim_Data' in current_channel:
+        h5_dataset = current_channel['nDim_Data']
+        reader = pyNSID.NSIDReader(h5_dataset.file.filename)
+        dataset = reader.read(h5_dataset)
+        dataset.h5_file = current_channel.file
+        return dataset
+    if 'Raw_Data' in current_channel:
+        if 'image_stack' in current_channel:
+            sid_dataset = sidpy.Dataset.from_array(np.swapaxes(current_channel['image_stack'][()], 2, 0))
+            dim_dir = ['SPATIAL', 'SPATIAL', 'TEMPORAL']
+        elif 'data' in current_channel:
+            sid_dataset = sidpy.Dataset.from_array(current_channel['data'][()])
+            dim_dir = ['SPATIAL', 'SPATIAL']
+        else:
+            size_x = int(current_channel['spatial_size_x'][()])
+            size_y = int(current_channel['spatial_size_y'][()])
+            if 'spectral_size_x' in current_channel:
+                size_s = int(current_channel['spectral_size_x'][()])
+            else:
+                size_s = 0
+            data = np.reshape(current_channel['Raw_Data'][()], (size_x, size_y, size_s))
+            sid_dataset = sidpy.Dataset.from_array(data)
+            if size_x > 1:
+                dim_dir.append('SPATIAL')
+            if size_y > 1:
+                dim_dir.append('SPATIAL')
+            if size_s > 1:
+                dim_dir.append('SPECTRAL')
+        sid_dataset.h5_dataset = current_channel['Raw_Data']
+
+    elif 'data' in current_channel:
+        sid_dataset = sidpy.Dataset.from_array(current_channel['data'][()])
+        dim_dir = ['SPATIAL', 'SPATIAL']
+        sid_dataset.h5_dataset = current_channel['data']
+    else:
+        return
+
+    if 'SPATIAL' in dim_dir:
+        if 'SPECTRAL' in dim_dir:
+            sid_dataset.data_type = sidpy.DataType.SPECTRAL_IMAGE
+        elif 'TEMPORAL' in dim_dir:
+            sid_dataset.data_type = sidpy.DataType.IMAGE_STACK
+        else:
+            sid_dataset.data_type = sidpy.DataType.IMAGE
+    else:
+        sid_dataset.data_type = sidpy.DataType.SPECTRUM
+
+    sid_dataset.quantity = 'intensity'
+    sid_dataset.units = 'counts'
+    if 'analysis' in current_channel:
+        sid_dataset.source = current_channel['analysis'][()]
+
+    set_dimensions(sid_dataset, current_channel)
+
+    return sid_dataset
+
+
+def set_dimensions(dset, current_channel):
+    """Attaches correct dimension from old pyTEMlib style.
+
+    Parameters
+    ----------
+    dset: sidpy.Dataset
+    current_channel: hdf5.Group
+    """
+    dim = 0
+    if dset.data_type == sidpy.DataType.IMAGE_STACK:
+        dset.set_dimension(dim, sidpy.Dimension(np.arange(dset.shape[dim]), name='frame',
+                                                units='frame', quantity='stack',
+                                                dimension_type='TEMPORAL'))
+        dim += 1
+    if 'IMAGE' in dset.data_type:
+
+        if 'spatial_scale_x' in current_channel:
+            scale_x = current_channel['spatial_scale_x'][()]
+        else:
+            scale_x = 1
+        if 'spatial_units' in current_channel:
+            units_x = current_channel['spatial_units'][()]
+            if len(units_x) < 2:
+                units_x = 'pixel'
+        else:
+            units_x = 'generic'
+        if 'spatial_scale_y' in current_channel:
+            scale_y = current_channel['spatial_scale_y'][()]
+        else:
+            scale_y = 0
+        dset.set_dimension(dim, sidpy.Dimension('x', np.arange(dset.shape[dim])*scale_x,
+                                                units=units_x, quantity='Length',
+                                                dimension_type='SPATIAL'))
+        dim += 1
+        dset.set_dimension(dim, sidpy.Dimension('y', np.arange(dset.shape[dim])*scale_y,
+                                                units=units_x, quantity='Length',
+                                                dimension_type='SPATIAL'))
+        dim += 1
+    if dset.data_type in [sidpy.DataType.SPECTRUM, sidpy.DataType.SPECTRAL_IMAGE]:
+        if 'spectral_scale_x' in current_channel:
+            scale_s = current_channel['spectral_scale_x'][()]
+        else:
+            scale_s = 1.0
+        if 'spectral_units_x' in current_channel:
+            units_s = current_channel['spectral_units_x']
+        else:
+            units_s = 'eV'
+
+        if 'spectral_offset_x' in current_channel:
+            offset = current_channel['spectral_offset_x']
+        else:
+            offset = 0.0
+        dset.set_dimension(dim, sidpy.Dimension(np.arange(dset.shape[dim]) * scale_s + offset,
+                                                name='energy',
+                                                units=units_s,
+                                                quantity='energy_loss',
+                                                dimension_type='SPECTRAL'))