302 lines
11 KiB
Python
302 lines
11 KiB
Python
import os
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import nixio as nix
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import numpy as np
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from enum import Enum
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from nixview.util.descriptors import FileDescriptor, ItemDescriptor
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class NodeType(Enum):
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Root = "root"
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Section = "Section"
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Block = "Block"
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DataArray = "Data Array"
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DataFrame = "Data Frame"
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Property = "Property"
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Dimension = "Dimension"
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Source = "Source"
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Tag = "Tag"
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MultiTag = "Multi Tag"
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Group = "Group"
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Feature="Feature"
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class Singleton(type):
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_instances = {}
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def __call__(cls, *args, **kwargs):
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if cls not in cls._instances:
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cls._instances[cls] = super(Singleton, cls).__call__(*args, **kwargs)
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return cls._instances[cls]
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class EntityBuffer():
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def __init__(self) -> None:
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super().__init__()
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self._buffer = {}
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def put(self, entity):
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if not hasattr(entity, "id"):
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return
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id = entity.id
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if id not in self._buffer.keys():
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self._buffer[id] = entity
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def has(self, id):
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return id in self._buffer.keys()
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def get(self, id):
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if self.has(id):
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return self._buffer[id]
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else:
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return None
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def clear(self):
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self._buffer.clear()
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class FileHandler(metaclass=Singleton):
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def __init__(self) -> None:
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super().__init__()
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self._filename = None
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self._nix_file = None
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self._file_requests = []
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self._entity_buffer = EntityBuffer()
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self._file_descriptor = None
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self._file_version = None
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def open(self, filename):
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self.close()
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if not os.path.exists(filename):
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return False, "File %s could not be found!" % filename
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try:
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self._nix_file = nix.File.open(filename, nix.FileMode.ReadOnly)
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self._filename = filename
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self._file_descriptor = FileDescriptor(self.filename, self._nix_file.format, self._nix_file.version,
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self._nix_file.created_at, self._nix_file.updated_at, os.path.getsize(self.filename)/1e+6)
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self.file_descriptor.block_count = len(self._nix_file.blocks)
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for b in self._nix_file.blocks:
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self.file_descriptor.data_array_count += len(b.data_arrays)
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self.file_descriptor.group_count += len(b.groups)
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self.file_descriptor.tag_count += len(b.tags)
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self.file_descriptor.tag_count += len(b.multi_tags)
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if hasattr(b, "data_frames"):
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self.file_descriptor.data_frame_count += len(b.data_frames)
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self._file_version = self._nix_file.version
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return True, "Successfully opened file %s." % filename.split(os.sep)[-1]
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except RuntimeError as e:
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return False, "Failed to open file %s! \n Error message is: %s" % (filename, e)
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except OSError as e:
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return False, "Failed to open file %s! \n Error message is: %s\n Probably no nix file?!" % (filename, e)
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def close(self):
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if self._nix_file is not None and self._nix_file.is_open():
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self._nix_file.close()
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self._nix_file = None
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self._file_requests = []
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self._entity_buffer.clear()
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self._file_descriptor = None
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self._file_version = None
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@property
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def file_descriptor(self):
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return self._file_descriptor
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@property
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def is_valid(self):
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return self._nix_file is not None and self._nix_file.is_open()
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@property
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def filename(self):
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return self._filename
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def valid_count(self, shape, offset, count):
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valid_count = np.empty(len(shape), dtype=int)
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for i, (o, c) in enumerate(zip(offset, count)):
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if o + c > shape[i]:
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valid_count[i] = shape[i] - o
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return valid_count
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def count_is_valid(self, shape, offset, count):
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res = True
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for s, o, c in zip(shape, offset, count):
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res = res and o + c <= s
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return res
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def request_data(self, entity_descriptor, offset=None, count=None):
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entity = self._entity_buffer.get(entity_descriptor.id)
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if entity is None:
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raise ValueError("Entity is invalid: %s" % entity_descriptor)
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if not self.count_is_valid(entity.shape, offset, count):
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count = self.valid_count(entity.shape, offset, count)
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seg = tuple([slice(o, o + c) for o, c in zip(offset, count)])
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return entity[seg]
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def request_section_descriptor(self, id):
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fs = self._entity_buffer.get(id)
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if fs is None:
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found_section = self._nix_file.find_sections(lambda s: s.id == id)
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fs = found_section[0] if len(found_section) > 0 else None
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if fs is None:
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return None
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else:
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item = ItemDescriptor(fs.name, fs.id, fs.type, definition=fs.definition, entity_type=NodeType.Section)
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return item
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def request_metadata(self, root_id=None, depth=1):
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"""[summary]
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Args:
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root_id ([type], optional): [description]. Defaults to None.
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depth (int, optional): [description]. Defaults to 1.
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"""
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def get_subsections(section):
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sub_sections = []
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for s in section.sections:
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self._entity_buffer.put(s)
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sub_sections.append(ItemDescriptor(s.name, s.id, s.type, definition=s.definition, entity_type=NodeType.Section))
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return sub_sections
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def get_properties(section):
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props = []
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for p in section.props:
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value = ""
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if self._file_version < (1,1,1):
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vals = p.values
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if len(vals) > 1:
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value += "["
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value += ",".join(map(str, [v.value for v in vals]))
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value += "]"
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else:
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value = str(vals[0].value)
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else:
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vals = p.values
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value += "["
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value += ",".join(map(str, [v.value for v in vals]))
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value += "]"
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if p.unit is not None:
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value += " " + p.unit
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props.append(ItemDescriptor(p.name, p.id, value=value, entity_type=NodeType.Property))
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return props
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sections = []
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properties = []
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if root_id is None:
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sections = get_subsections(self._nix_file)
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else:
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fs = self._entity_buffer.get(root_id)
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if fs is None:
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found_section = self._nix_file.find_sections(lambda s: s.id == root_id)
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fs = found_section[0] if len(found_section) > 0 else None
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if fs is None:
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return sections, properties
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sections.extend(get_subsections(fs))
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properties.extend(get_properties(fs))
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return sections, properties
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def _entity_info(self, entities, block_id, entity_type):
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infos = []
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for e in entities:
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self._entity_buffer.put(e)
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itd = ItemDescriptor(e.name, e.id, e.type, definition=e.definition, entity_type=entity_type, block_id=block_id)
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section = e.metadata if hasattr(e, "metadata") else None
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itd.metadata_id = section.id if section is not None else None
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itd.data_type = e.data_type if hasattr(e, "data_type") else None
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itd.created_at = e.created_at if hasattr(e, "created_at") else None
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itd.updated_at = e.updated_at if hasattr(e, "updated") else None
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itd.shape = e.shape if hasattr(e, "shape") else None
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src = e.source if hasattr(e, "source") else None
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itd.source_id = src.id if src is not None else None
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infos.append(itd)
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if entity_type == NodeType.DataArray:
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itd.value = "%s %s entries" % (str(e.shape), e.dtype)
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elif entity_type == NodeType.Tag:
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point_or_segment = "segment" if e.extent else "point"
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start = str(e.position)
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end = ("to " + str(tuple(np.array(e.position) + np.array(e.extent)))) if e.extent else ""
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itd.value = "tags %s %s %s" %(point_or_segment, start, end)
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# TODO set the value to something meaningful for the various entity types
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return infos
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def request_blocks(self):
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return self._entity_info(self._nix_file.blocks, None, NodeType.Block)
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def get_block(self, id):
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b = b = self._entity_buffer.get(id)
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if not b:
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b = self._nix_file.blocks[id]
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return b
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def request_data_arrays(self, block_id):
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b = self.get_block(block_id)
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return self._entity_info(b.data_arrays, block_id, NodeType.DataArray)
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def request_tags(self, block_id):
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b = self.get_block(block_id)
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tags = self._entity_info(b.tags, block_id, NodeType.Tag)
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tags.extend(self._entity_info(b.multi_tags, block_id, NodeType.MultiTag))
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return tags
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def request_references(self, block_id, tag_id, is_mtag):
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b = self.get_block(block_id)
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t = self._entity_buffer.get(tag_id)
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if t is None:
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if is_mtag:
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t = b.multi_tags[tag_id]
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else:
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t = b.tags[tag_id]
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return self._entity_info(t.references, block_id, NodeType.DataArray)
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def request_features(self, block_id, tag_id, is_mtag):
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b = self.get_block(block_id)
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t = self._entity_buffer.get(tag_id)
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if t is None:
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if is_mtag:
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t = b.multi_tags[tag_id]
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else:
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t = b.tags[tag_id]
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feats = []
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for f in t.features:
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itd = ItemDescriptor(f.data.name, f.id, f.link_type, definition=f.data.definition, block_id=block_id, entity_type=NodeType.Feature)
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feats.append(itd)
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return feats
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def request_dimensions(self, block_id, array_id):
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da = self._entity_buffer.get(array_id)
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if da is None:
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b = self.get_block(block_id)
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da = b.data_arrays[array_id]
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dimensions = []
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for i, d in enumerate(da.dimensions):
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dim_name = "%i. dim: %s" % (i+1, d.label if hasattr(d, "label") else "")
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dim_type= "%s %s" % (d.dimension_type, "dimension")
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dimensions.append(ItemDescriptor(dim_name, type=dim_type, entity_type=NodeType.Dimension, block_id=block_id))
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return dimensions
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def request_data_frames(self, block_id):
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if self._nix_file.version[1] >= 2:
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b = self.get_block(block_id)
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return self._entity_info(b.data_frames, block_id, NodeType.DataFrame)
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return []
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def request_groups(self, block_id):
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b = self.get_block(block_id)
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return self._entity_info(b.groups, block_id, NodeType.Group)
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def request_sources(self, block_id, parent_source_id=None):
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def get_subsources(src):
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sub_sources = []
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for s in src.sources:
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self._entity_buffer.put(s)
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sub_sources.append(ItemDescriptor(s.name, s.id, s.type, definition=s.definition, entity_type=NodeType.Source))
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return sub_sources
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b = self.get_block(block_id)
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if parent_source_id is None:
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return self._entity_info(b.sources, block_id, NodeType.Source)
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else:
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srcs = b.find_sources(lambda s: s.id == parent_source_id)
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sources = []
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for src in srcs:
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sources.extend(get_subsources(src))
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return sources |