forked from jgrewe/fishbook
136 lines
4.2 KiB
Python
136 lines
4.2 KiB
Python
from functools import reduce
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import numpy as np
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import nixio as nix
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import os
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import glob
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import datetime as dt
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from IPython import embed
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def read_info_file(file_name):
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"""
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Reads the info file and returns the stored metadata in a dictionary. The dictionary may be nested.
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@param file_name: The name of the info file.
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@return: dictionary, the stored information.
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"""
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root = {}
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with open(file_name, 'r') as f:
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lines = f.readlines()
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for l in lines:
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if not l.startswith("#"):
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continue
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l = l.strip("#").strip()
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if len(l) == 0:
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continue
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if not ": " in l: # subsection
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sec = {}
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root[l[:-1] if l.endswith(":") else l] = sec
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else:
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parts = l.split(': ')
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sec[parts[0].strip()] = parts[1].strip('"').strip()
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return root
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def find_key_recursive(dictionary, key, path=[]):
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assert(isinstance(dictionary, dict))
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if key in dictionary.keys():
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path.append(key)
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return True
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for k in dictionary.keys():
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if isinstance(dictionary[k], dict):
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if find_key_recursive(dictionary[k], key, path):
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path.insert(-1, k)
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break
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return len(path) > 0
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def deep_get(dictionary, keys, default=None):
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assert(isinstance(dictionary, dict))
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assert(isinstance(keys, list))
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return reduce(lambda d, key: d.get(key, default) if isinstance(d, dict) else default, keys, dictionary)
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def read_dataset_info(info_file):
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exp = ""
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quality = ""
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comment = ""
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rec_date = None
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has_nix = False
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if not os.path.exists(info_file):
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return exp, rec_date, quality, comment, has_nix
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has_nix = len(glob.glob(os.path.sep.join(info_file.split(os.path.sep)[:-1]) + os.path.sep + "*.nix")) > 0
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info = read_info_file(info_file)
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p = []
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find_key_recursive(info, "Experimenter", p)
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if len(p) > 0:
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exp = deep_get(info, p)
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p = []
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find_key_recursive(info, "Date", p)
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if len(p) > 0:
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rec_date = dt.date.fromisoformat(deep_get(info, p))
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p = []
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find_key_recursive(info, "Recording quality", p)
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if len(p) > 0:
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quality = deep_get(info, p)
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find_key_recursive(info, "Comment", p)
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if len(p) > 0:
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comment = deep_get(info, p, default="")
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return exp, rec_date, quality, comment, has_nix
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def nix_metadata_to_dict(section):
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info = {}
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for p in section.props:
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info[p.name] = [v.value for v in p.values]
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for s in section.sections:
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info[s.name] = nix_metadata_to_dict(s)
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return info
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def nix_metadata_to_yaml(section, cur_depth=0, val_count=1):
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assert(isinstance(section, nix.section.SectionMixin))
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yaml = "%s%s:\n" % ("\t" * cur_depth, section.name)
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for p in section.props:
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val_str = ""
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if val_count > 1 and len(p.values) > 1:
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val_str = "[" + ', '.join([v.to_string() for v in p.values]) + "]"
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elif len(p.values) == 1:
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val_str = p.values[0].to_string()
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yaml += "%s%s: %s\n" % ("\t" * (cur_depth+1), p.name, val_str)
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for s in section.sections:
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yaml += nix_metadata_to_yaml(s, cur_depth+1)
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return yaml
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def find_mtags_for_tag(block, tag):
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assert(isinstance(block, nix.pycore.block.Block))
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assert(isinstance(tag, nix.pycore.tag.Tag))
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mtags = []
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tag_start = np.atleast_1d(tag.position)
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tag_end = tag_start + np.atleast_1d(tag.extent)
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for mt in block.multi_tags:
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mt_start = np.atleast_1d(mt.positions[0, :])
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mt_end = np.atleast_1d(mt.positions[-1, :] + mt.extents[-1, :])
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in_tag = True
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for i in range(len(tag_start)):
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if mt_start[i] < tag_start[i] or mt_end[i] > tag_end[i]:
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in_tag = False
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break
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if in_tag:
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mtags.append(mt)
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return mtags
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if __name__ == "__main__":
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nix_file = "../../science/high_freq_chirps/data/2018-11-09-aa-invivo-1/2018-11-09-aa-invivo-1.nix"
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f = nix.File.open(nix_file, nix.FileMode.ReadOnly)
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b = f.blocks[0]
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yml = nix_metadata_to_yaml(b.tags[0].metadata)
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print(yml)
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print("-"* 80)
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print(nix_metadata_to_yaml(b.metadata))
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embed()
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f.close()
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