[tonix] adding script that adds all the data arrays to nix
This commit is contained in:
parent
e61172227e
commit
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@ -1,711 +1,138 @@
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import logging
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import logging
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import pathlib
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import pathlib
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import tomllib
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import matplotlib.pyplot as plt
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import nixio
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import nixio
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import numpy as np
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import numpy as np
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import rlxnix as rlx
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import rlxnix as rlx
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from IPython import embed
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from IPython import embed
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from neo.io import OpenEphysBinaryIO
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from neo.io import OpenEphysBinaryIO
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from nixio.exceptions import DuplicateName
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from scipy import signal
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from oephys2nix.logging import setup_logging
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from oephys2nix.metadata import create_dict_from_section, create_metadata_from_dict
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log = logging.getLogger(__name__)
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log = logging.getLogger(__name__)
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setup_logging(log, level="DEBUG")
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setup_logging(log, level="DEBUG")
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class CreateNix:
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class RawToNix:
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def __init__(self, open_ephys_path, relacs_nix_path, nix_file):
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def __init__(self, open_ephys_path: pathlib.Path, relacs_nix_path: str, nix_file: str):
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self.relacs_nix_file = nixio.File.open(relacs_nix_path, nixio.FileMode.ReadOnly)
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self.relacs_nix_file = nixio.File.open(relacs_nix_path, nixio.FileMode.ReadOnly)
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self.dataset = rlx.Dataset(relacs_nix_path)
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self.dataset = rlx.Dataset(relacs_nix_path)
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self.relacs_block = self.relacs_nix_file.blocks[0]
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self.relacs_block = self.relacs_nix_file.blocks[0]
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self.relacs_sections = self.relacs_nix_file.sections
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self.relacs_sections = self.relacs_nix_file.sections
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self.spike_sorter_path = str(self.recording_path.resolve() / "spikesorter.nix")
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self.neo_data = OpenEphysBinaryIO(open_ephys_path).read(lazy=True)
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self.neo_data = OpenEphysBinaryIO(open_ephys_path).read(lazy=True)
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self.nix_file = nix_file
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self.nix_file = nixio.File(nix_file, nixio.FileMode.ReadWrite)
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self.nix_file.create_block("open-ephys.data", "open-ephys.sampled")
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self.block = self.nix_file.blocks[0]
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self.block = self.nix_file.blocks[0]
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def _load_config(self):
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def append_section(self):
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config_path = self.recording_path / "stimulus_config.toml"
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sec = self.nix_file.create_section(
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if not config_path.is_file():
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self.relacs_sections[0].name, self.relacs_sections[0].type
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log.debug("Stimulus config was not found")
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with open(config_path, "rb") as config_file:
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try:
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config = tomllib.load(config_file)
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config_file.close()
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return config
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except tomllib.TOMLDecodeError as e:
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config_file.close()
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raise tomllib.TOMLDecodeError(f"Error parsing TOML file: {e}")
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def _append_relacs_tag_mtags(self):
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for t in self.relacs_block.tags:
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log.debug(f"Appending relacs tags {t.name}")
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tag = self.block.create_tag(f"relacs_{t.name}", t.type, position=t.position)
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tag.extent = t.extent
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tag.references.extend(self.block.groups["relacs"].data_arrays)
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sec = self.relacs_sections[f"{t.name}"]
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d = create_dict_from_section(sec)
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try:
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new_sec = self.nix_file.create_section(sec.name, sec.type)
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create_metadata_from_dict(d, new_sec)
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except DuplicateName:
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pass
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tag.metadata = self.nix_file.sections[sec.name]
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for t in self.relacs_block.multi_tags:
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log.debug(f"Appending relacs multi-tags {t.name}")
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mtag = self.block.create_multi_tag(
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f"relacs_{t.name}",
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t.type,
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positions=t.positions[:],
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extents=t.extents[:],
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)
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mtag.references.extend(self.block.groups["relacs"].data_arrays)
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sec = self.relacs_sections[f"{t.name}"]
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d = create_dict_from_section(sec)
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try:
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new_sec = self.nix_file.create_section(sec.name, sec.type)
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create_metadata_from_dict(d, new_sec)
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except DuplicateName:
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pass
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mtag.metadata = self.nix_file.sections[sec.name]
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def _find_peak_ttl(self, time_ttl, peaks_ttl, lower, upper):
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peak = time_ttl[
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peaks_ttl[(time_ttl[peaks_ttl] > lower) & (time_ttl[peaks_ttl] < upper)]
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]
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if not peak.size > 0:
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log.error("No peaks found")
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elif peak.size > 1:
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if np.all(np.diff(peak) > 0.5):
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log.error("Peaks are further aways than 0.5 seconds")
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log.error(f"Peaks {peak}, Furthest aways: {np.max(peak)}")
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peak = np.mean(peak)
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return peak
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def _find_peak_ttl_index(self, time_ttl, peaks_ttl, current_position):
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new_repro_start_index = peaks_ttl[
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(time_ttl[peaks_ttl] > current_position - 0.1)
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& (time_ttl[peaks_ttl] < current_position + 0.1)
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]
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# if multiple take the last one
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if new_repro_start_index.size > 1:
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log.warning("Multiple current positions taking the last index")
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new_repro_start_index = new_repro_start_index[-1]
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# log.debug(f"Time current repro/trial {time_ttl[new_repro_start_index]}")
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if np.where(new_repro_start_index == peaks_ttl)[0] + 1 == len(peaks_ttl):
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return np.array([])
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else:
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next_repro_start = peaks_ttl[
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np.where(new_repro_start_index == peaks_ttl)[0] + 1
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]
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start_next_repro = time_ttl[next_repro_start]
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log.debug(f"Start of new repro/trial {start_next_repro}")
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return start_next_repro
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def _reference_groups(self) -> list[nixio.Group]:
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return [
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self.block.groups["neuronal-data"],
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# self.block.groups["spike-data"],
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self.block.groups["efish"],
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self.block.groups["relacs"],
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]
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def _append_mtag(self, repro, positions, extents):
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try:
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nix_mtag = self.block.create_multi_tag(
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f"{repro.name}",
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"relacs.stimulus",
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positions=positions,
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extents=extents,
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)
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except DuplicateName:
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del self.block.multi_tags[repro.name]
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nix_mtag = self.block.create_multi_tag(
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f"{repro.name}",
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"relacs.stimulus",
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positions=positions,
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extents=extents,
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)
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sec = self.relacs_sections[f"{repro.name}"]
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d = create_dict_from_section(sec)
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try:
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new_sec = self.nix_file.create_section(sec.name, sec.type)
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create_metadata_from_dict(d, new_sec)
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except DuplicateName:
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del self.nix_file.sections[sec.name]
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new_sec = self.nix_file.create_section(sec.name, sec.type)
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create_metadata_from_dict(d, new_sec)
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nix_mtag.metadata = self.nix_file.sections[repro.name]
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[
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nix_mtag.references.extend(ref_groups.data_arrays)
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for ref_groups in self._reference_groups
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if ref_groups.data_arrays
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]
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try:
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nix_group = self.block.create_group(repro.name, repro.type)
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except DuplicateName:
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nix_group = self.nix_file.blocks[0].groups[repro.name]
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nix_group.multi_tags.append(nix_mtag)
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def _append_tag(self, repro, position, extent):
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try:
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nix_tag = self.block.create_tag(
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f"{repro.name}",
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"relacs.repro_run",
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position=np.array(position).flatten(),
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)
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nix_tag.extent = extent.flatten()
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except DuplicateName:
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del self.block.tags[repro.name]
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nix_tag = self.block.create_tag(
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f"{repro.name}",
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"relacs.repro_run",
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position=np.array(position).flatten(),
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)
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nix_tag.extent = extent.flatten()
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sec = self.relacs_sections[f"{repro.name}"]
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d = create_dict_from_section(sec)
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try:
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new_sec = self.nix_file.create_section(sec.name, sec.type)
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create_metadata_from_dict(d, new_sec)
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except DuplicateName:
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del self.nix_file.sections[sec.name]
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new_sec = self.nix_file.create_section(sec.name, sec.type)
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create_metadata_from_dict(d, new_sec)
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nix_tag.metadata = self.nix_file.sections[repro.name]
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# NOTE: adding refs to tag
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[
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nix_tag.references.extend(ref_groups.data_arrays)
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for ref_groups in self._reference_groups
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if ref_groups.data_arrays
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]
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try:
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nix_group = self.block.create_group(repro.name, repro.type)
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except DuplicateName:
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nix_group = self.nix_file.blocks[0].groups[repro.name]
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nix_group.tags.append(nix_tag)
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def create_repros_automatically(self):
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ttl_oeph = self.block.data_arrays["ttl-line"][:]
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time_ttl = np.arange(len(ttl_oeph)) / self.cfg.open_ephys.samplerate
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time_index = np.arange(len(ttl_oeph))
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# Threshold for TTL peak
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threshold = 2
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peaks_ttl = time_index[
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(np.roll(ttl_oeph, 1) < threshold) & (ttl_oeph > threshold)
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]
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# WARNING:Check if peaks are duplicates or near each other
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close_peaks = np.where(np.diff(peaks_ttl) == 1)[0]
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if close_peaks.size > 0:
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peaks_ttl = np.delete(peaks_ttl, close_peaks)
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# NOTE: Get the first peak from the toml file
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first_peak = self._find_peak_ttl(
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time_ttl,
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peaks_ttl,
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self.stimulus_config["stimulus"]["start_repro_low"],
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self.stimulus_config["stimulus"]["start_repro_high"],
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)
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)
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d = create_dict_from_section(self.relacs_sections[0])
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create_metadata_from_dict(d, sec)
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self.block.metadata = sec
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current_position = np.asarray(first_peak.reshape(1))
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def append_fish_lines(self):
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# NOTE: Start defined by config
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efishs = [
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for i, repro in enumerate(
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"ttl-line",
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self.dataset.repro_runs()[
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"global-eod",
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self.stimulus_config["stimulus"]["repro_number_start"] :
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"stimulus",
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],
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"local-eod",
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start=self.stimulus_config["stimulus"]["repro_number_start"],
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):
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log.debug(repro.name)
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log.debug(f"Current Position {current_position.item()}")
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if repro.duration < 1.0:
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log.warning(f"Skipping repro {repro.name} because it is two short")
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continue
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if repro.stimuli:
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log.debug("Processing MultiTag")
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repetition = len(repro.stimuli)
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extents_mtag = np.zeros((repetition, 1))
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position_mtags = np.zeros((repetition, 1))
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for trial, stimulus in enumerate(repro.stimuli):
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duration_trial = stimulus.duration
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extents_mtag[trial] = duration_trial
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position_mtags[trial] = current_position
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current_position = self._find_peak_ttl_index(
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time_ttl, peaks_ttl, current_position
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)
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# current_position = position_mtags[-1]
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self._append_mtag(repro, position_mtags, extents_mtag)
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extent = position_mtags[-1] + extents_mtag[-1] - position_mtags[0]
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self._append_tag(repro, position_mtags[0], extent)
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if not current_position.size > 0:
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log.info("Finishing writing")
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log.info("Closing nix files")
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self.close()
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exit()
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else:
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if i == 0 and "BaselineActivity" in repro.name:
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self._append_tag(repro, 0.0, current_position)
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continue
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last_repro_name = self.dataset.repro_runs()[i - 1].name
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last_repro_position = (
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self.block.groups[last_repro_name].tags[0].position[0]
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+ self.block.groups[last_repro_name].tags[0].extent[0]
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)
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self._append_tag(
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repro,
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last_repro_position.reshape(-1, 1),
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(current_position - last_repro_position).reshape(-1, 1),
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)
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self.close()
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#
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#
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# # NOTE: Create a repro tag
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# t = self.block.create_tag(
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# f"{repro.name}",
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# f"{repro.type}",
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# position=current_position,
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# )
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# t.metadata = repro.metadata
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#
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# for i, group in enumerate(
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# list(self.relacs_block.groups)[
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# self.stimulus_config["stimulus"]["repro_number_start"] :
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# ],
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# start=self.stimulus_config["stimulus"]["repro_number_start"],
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# ):
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# log.debug(group.name)
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# log.debug(current_position)
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#
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# nix_group = self.block.groups[group.name]
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# if group.name == "BaselineActivity_1":
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# first_peak = 0.0
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# current_position = np.array(first_peak).reshape(1)
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#
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# # if no multi_tag exists just a tag
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# if not group.multi_tags:
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# log.debug(f"Creating Tag {group.name}")
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# t = self.block.create_tag(
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# f"{nix_group.name}",
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# f"{nix_group.type}",
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# position=current_position,
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# )
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# t.metadata = self.nix_file.sections[group.name]
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#
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# # searching for the end of the repro in the ttl channel
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# start_next_repro = time_ttl[
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# peaks_ttl[
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# (
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# time_ttl[peaks_ttl]
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# > group.tags[0].extent + current_position - 1
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# )
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# & (
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# time_ttl[peaks_ttl]
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# < group.tags[0].extent + current_position + 1
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# )
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# ]
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# ]
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# log.debug(start_next_repro)
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# if start_next_repro.size > 1:
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|
||||||
# if np.all(np.diff(start_next_repro) > 0.5):
|
|
||||||
# log.error("Wrong end point in end of repro")
|
|
||||||
# log.error(f"{start_next_repro}, {np.max(start_next_repro)}")
|
|
||||||
# start_next_repro = np.mean(start_next_repro)
|
|
||||||
#
|
|
||||||
# if not start_next_repro:
|
|
||||||
# log.error(f"No Endpoint found for repro {group.name}")
|
|
||||||
# embed()
|
|
||||||
# exit()
|
|
||||||
# t.extent = (start_next_repro - t.position[0]).reshape(1)
|
|
||||||
# # add references to the tag
|
|
||||||
# [
|
|
||||||
# t.references.extend(ref_group.data_arrays)
|
|
||||||
# for ref_group in referencs_groups
|
|
||||||
# if ref_group.data_arrays
|
|
||||||
# ]
|
|
||||||
# nix_group.tags.append(t)
|
|
||||||
# current_position = start_next_repro.reshape(1)
|
|
||||||
#
|
|
||||||
# else:
|
|
||||||
# # NOTE: If repro has multitags
|
|
||||||
# log.debug(f"Creating Multi Tag {group.name}")
|
|
||||||
# test_mul_tags = group.multi_tags[0].positions[:]
|
|
||||||
# test_position_tag, test_extent_tag = (
|
|
||||||
# group.tags[0].position[0],
|
|
||||||
# group.tags[0].extent[0],
|
|
||||||
# )
|
|
||||||
# len_mtag = len(
|
|
||||||
# test_mul_tags[
|
|
||||||
# (test_mul_tags >= test_position_tag)
|
|
||||||
# & (test_mul_tags <= (test_position_tag + test_extent_tag))
|
|
||||||
# ]
|
|
||||||
# )
|
|
||||||
# extents_mtag = group.multi_tags[0].extents[:][
|
|
||||||
# (test_mul_tags >= test_position_tag)
|
|
||||||
# & (test_mul_tags <= (test_position_tag + test_extent_tag))
|
|
||||||
# ]
|
|
||||||
# position_mtags = np.zeros((len_mtag, 1))
|
|
||||||
# position_mtags[0] = current_position
|
|
||||||
#
|
|
||||||
# for j, extents in enumerate(extents_mtag[1:], start=1):
|
|
||||||
# next_repro_position = time_ttl[
|
|
||||||
# peaks_ttl[
|
|
||||||
# (
|
|
||||||
# time_ttl[peaks_ttl]
|
|
||||||
# > extents + current_position - extents / 2
|
|
||||||
# )
|
|
||||||
# & (time_ttl[peaks_ttl] < extents + current_position + 2)
|
|
||||||
# ]
|
|
||||||
# ]
|
|
||||||
# if next_repro_position.size == 0:
|
|
||||||
# log.error(f"next start of MultiTag not found")
|
|
||||||
# embed()
|
|
||||||
# exit()
|
|
||||||
#
|
|
||||||
# if next_repro_position.size > 1:
|
|
||||||
# if np.all(np.diff(next_repro_position) > 0.005):
|
|
||||||
# log.error("Wrong end point in end of repro")
|
|
||||||
# log.error(
|
|
||||||
# f"{next_repro_position}, {np.max(next_repro_position)}"
|
|
||||||
# )
|
|
||||||
# embed()
|
|
||||||
# exit()
|
|
||||||
# exit(1)
|
|
||||||
# next_repro_position = np.mean(next_repro_position)
|
|
||||||
# log.debug(f"{j}, {next_repro_position}")
|
|
||||||
#
|
|
||||||
# position_mtags[j] = next_repro_position
|
|
||||||
# current_position = next_repro_position
|
|
||||||
#
|
|
||||||
# start_next_repro = time_ttl[
|
|
||||||
# peaks_ttl[
|
|
||||||
# (time_ttl[peaks_ttl] > current_position + nix_mtag.extents[-1])
|
|
||||||
# & (
|
|
||||||
# time_ttl[peaks_ttl]
|
|
||||||
# < current_position + nix_mtag.extents[-1] + 2
|
|
||||||
# )
|
|
||||||
# ]
|
|
||||||
# ]
|
|
||||||
# if not start_next_repro.size == 0:
|
|
||||||
# if start_next_repro.size > 1:
|
|
||||||
# if np.all(np.diff(start_next_repro) > 0.005):
|
|
||||||
# log.error("Wrong end point in end of repro")
|
|
||||||
# log.error(f"{start_next_repro}, {np.max(start_next_repro)}")
|
|
||||||
# embed()
|
|
||||||
# exit(1)
|
|
||||||
#
|
|
||||||
# start_next_repro = np.mean(start_next_repro)
|
|
||||||
#
|
|
||||||
# else:
|
|
||||||
# log.debug(
|
|
||||||
# "No ttl pluse foud for the end of the repro create time point"
|
|
||||||
# )
|
|
||||||
# log.debug("Taking the next ttl pulse")
|
|
||||||
# new_repro_start_index = peaks_ttl[
|
|
||||||
# (time_ttl[peaks_ttl] > current_position - 1)
|
|
||||||
# & (time_ttl[peaks_ttl] < current_position + 2)
|
|
||||||
# ]
|
|
||||||
#
|
|
||||||
# # if multiple take the last one
|
|
||||||
# if new_repro_start_index.size > 1:
|
|
||||||
# new_repro_start_index = new_repro_start_index[-1]
|
|
||||||
#
|
|
||||||
# log.debug(time_ttl[new_repro_start_index])
|
|
||||||
# try:
|
|
||||||
# next_repro_start = peaks_ttl[
|
|
||||||
# np.where(new_repro_start_index == peaks_ttl)[0] + 1
|
|
||||||
# ]
|
|
||||||
# except IndexError:
|
|
||||||
# if np.where(new_repro_start_index == peaks_ttl)[0] + 1 == len(
|
|
||||||
# peaks_ttl
|
|
||||||
# ):
|
|
||||||
# log.debug("Finishing writing")
|
|
||||||
# self.nix_file.close()
|
|
||||||
# self.relacs_nix_file.close()
|
|
||||||
# exit(1)
|
|
||||||
# if next_repro_start.size > 1:
|
|
||||||
# log.debug("Start of next Repro has multiple ttl pulse")
|
|
||||||
# embed()
|
|
||||||
# exit()
|
|
||||||
#
|
|
||||||
# # check if the time difference is greater and 5 seconds
|
|
||||||
# if (
|
|
||||||
# not time_ttl[next_repro_start] - time_ttl[new_repro_start_index]
|
|
||||||
# > 5
|
|
||||||
# ):
|
|
||||||
# log.error("Wrong endpoint for repro")
|
|
||||||
# exit(1)
|
|
||||||
# start_next_repro = time_ttl[next_repro_start]
|
|
||||||
# log.info(f"Start of new Repro {start_next_repro}")
|
|
||||||
#
|
|
||||||
# current_position = start_next_repro
|
|
||||||
#
|
|
||||||
# # NOTE: If SAM or Baseline we dont have to find the next current position
|
|
||||||
# if (
|
|
||||||
# group.name.split("_")[0] == "SAM"
|
|
||||||
# or group.name.split("_")[0] == "BaselineActivity"
|
|
||||||
# # or group.name.split("_")[0] == "FileStimulus"
|
|
||||||
# ):
|
|
||||||
# current_position = current_position.reshape(1)
|
|
||||||
# log.info(f"Start of new Repro {current_position}")
|
|
||||||
# continue
|
|
||||||
#
|
|
||||||
# # peaks_repro_index = peaks_ttl[
|
|
||||||
# # (time_ttl[peaks_ttl] > current_position - 1)
|
|
||||||
# # & (time_ttl[peaks_ttl] < current_position + 2)
|
|
||||||
# # ]
|
|
||||||
# #
|
|
||||||
# # # if multiple take the last one
|
|
||||||
# # if peaks_repro_index.size > 1:
|
|
||||||
# # peaks_repro_index = peaks_repro_index[-1]
|
|
||||||
# #
|
|
||||||
# # log.debug(time_ttl[peaks_repro_index])
|
|
||||||
# # next_repro_start = peaks_ttl[
|
|
||||||
# # np.where(peaks_repro_index == peaks_ttl)[0] + 1
|
|
||||||
# # ]
|
|
||||||
# # if next_repro_start.size > 1:
|
|
||||||
# # embed()
|
|
||||||
# #
|
|
||||||
# # # check if the time difference is greater and 5 seconds
|
|
||||||
# # if not time_ttl[next_repro_start] - time_ttl[peaks_repro_index] > 5:
|
|
||||||
# # log.error("Wrong endpoint for repro")
|
|
||||||
# # embed()
|
|
||||||
# # exit()
|
|
||||||
# # current_position = time_ttl[next_repro_start]
|
|
||||||
# # log.info(f"Start of new Repro {current_position}")
|
|
||||||
# #
|
|
||||||
# # current_position = current_position.reshape(1)
|
|
||||||
#
|
|
||||||
# self.nix_file.close()
|
|
||||||
# self.relacs_nix_file.close()
|
|
||||||
|
|
||||||
def create_repros_from_config_file(
|
|
||||||
self,
|
|
||||||
):
|
|
||||||
ttl_oeph = self.block.data_arrays["ttl-line"][:]
|
|
||||||
peaks_ttl = signal.find_peaks(
|
|
||||||
ttl_oeph.flatten(),
|
|
||||||
**self.stimulus_config["stimulus"]["peak_detection"],
|
|
||||||
)[0]
|
|
||||||
time_ttl = np.arange(len(ttl_oeph)) / self.cfg.open_ephys.samplerate
|
|
||||||
|
|
||||||
number_of_repros = len(self.stimulus_config["repros"]["name"])
|
|
||||||
|
|
||||||
referencs_groups = [
|
|
||||||
self.block.groups["neuronal-data"],
|
|
||||||
self.block.groups["spike-data"],
|
|
||||||
self.block.groups["efish"],
|
|
||||||
]
|
]
|
||||||
|
|
||||||
for repro_index in range(number_of_repros):
|
efish_types = [
|
||||||
name = self.stimulus_config["repros"]["name"][repro_index]
|
"open-ephys.data.sampled",
|
||||||
log.debug(name)
|
"open-ephys.data.sampled",
|
||||||
start = np.array(self.stimulus_config["repros"]["start"][repro_index])
|
"open-ephys.data.sampled",
|
||||||
end = np.array(self.stimulus_config["repros"]["end"][repro_index])
|
"open-ephys.data.sampled",
|
||||||
nix_group = self.block.groups[name]
|
]
|
||||||
if start.size > 1:
|
|
||||||
start_repro = time_ttl[
|
|
||||||
peaks_ttl[
|
|
||||||
(time_ttl[peaks_ttl] > start[0])
|
|
||||||
& (time_ttl[peaks_ttl] < start[1])
|
|
||||||
]
|
|
||||||
]
|
|
||||||
if start_repro.size > 1:
|
|
||||||
if np.all(np.diff(start_repro) > 0.005):
|
|
||||||
log.error("Wrong end point in end of repro")
|
|
||||||
log.error(f"{name[repro_index]}, {np.max(start_repro)}")
|
|
||||||
exit(1)
|
|
||||||
start_repro = np.mean(start_repro)
|
|
||||||
else:
|
|
||||||
start_repro = start_repro[0]
|
|
||||||
else:
|
|
||||||
start_repro = start[0]
|
|
||||||
|
|
||||||
if end.size > 1:
|
efish_group = self.block.create_group("efish", "open-ephys.sampled")
|
||||||
end_repro = time_ttl[
|
|
||||||
peaks_ttl[
|
|
||||||
(time_ttl[peaks_ttl] > end[0]) & (time_ttl[peaks_ttl] < end[1])
|
|
||||||
]
|
|
||||||
]
|
|
||||||
if end_repro.size > 1:
|
|
||||||
if np.all(np.diff(end_repro) > 0.005):
|
|
||||||
log.error("Wrong end point in end of repro")
|
|
||||||
log.error(f"{name[repro_index]}, {np.max(end_repro)}")
|
|
||||||
exit(1)
|
|
||||||
end_repro = np.mean(end_repro)
|
|
||||||
else:
|
|
||||||
end_repro = end[0]
|
|
||||||
|
|
||||||
nix_tag = self.block.create_tag(
|
efish_neo_data = self.neo_data[0].segments[0].analogsignals[1].load()
|
||||||
f"{nix_group.name}",
|
|
||||||
f"{nix_group.type}",
|
for i in np.arange(len(efishs)):
|
||||||
position=[start_repro],
|
log.debug(f"Appending efish traces {efishs[i]}")
|
||||||
|
efish_neo_data_array = efish_neo_data[:, i]
|
||||||
|
data_array = self.block.create_data_array(
|
||||||
|
f"{efishs[i]}",
|
||||||
|
f"{efish_types[i]}",
|
||||||
|
data=efish_neo_data_array.magnitude.flatten(),
|
||||||
|
label="voltage",
|
||||||
|
unit="V",
|
||||||
)
|
)
|
||||||
nix_tag.extent = [end_repro - start_repro]
|
data_array.append_sampled_dimension(
|
||||||
nix_tag.metadata = self.nix_file.sections[name]
|
1 / efish_neo_data.sampling_rate.magnitude, label="time", unit="s"
|
||||||
|
|
||||||
# NOTE: adding refs to tag
|
|
||||||
[
|
|
||||||
nix_tag.references.extend(ref_groups.data_arrays)
|
|
||||||
for ref_groups in referencs_groups
|
|
||||||
if ref_groups.data_arrays
|
|
||||||
]
|
|
||||||
nix_group.tags.append(nix_tag)
|
|
||||||
|
|
||||||
if not self.relacs_block.groups[name].multi_tags:
|
|
||||||
log.debug(f"no multitags in repro {name}, skipping")
|
|
||||||
continue
|
|
||||||
|
|
||||||
start_repro_multi_tag = start_repro.copy()
|
|
||||||
positions = []
|
|
||||||
positions.append(np.array(start_repro))
|
|
||||||
extents = []
|
|
||||||
extents_relacsed_nix = (
|
|
||||||
self.relacs_block.groups[name].multi_tags[0].extents[:]
|
|
||||||
)
|
)
|
||||||
extents.append(np.array(extents_relacsed_nix[0]))
|
efish_group.data_arrays.append(data_array)
|
||||||
index_multi_tag = 0
|
|
||||||
while start_repro_multi_tag < end_repro:
|
|
||||||
log.debug(f"{start_repro_multi_tag}")
|
|
||||||
|
|
||||||
start_repro_multi_tag = time_ttl[
|
def append_relacs_lines(self):
|
||||||
peaks_ttl[
|
relacs = [
|
||||||
(
|
"V-1",
|
||||||
time_ttl[peaks_ttl]
|
"EOD",
|
||||||
> start_repro_multi_tag
|
"LocalEOD-1",
|
||||||
+ extents_relacsed_nix[index_multi_tag]
|
"GlobalEFieldStimulus",
|
||||||
)
|
"Spikes-1",
|
||||||
& (
|
"Chirps",
|
||||||
time_ttl[peaks_ttl]
|
"LocalBeat-1-1",
|
||||||
< start_repro_multi_tag
|
]
|
||||||
+ extents_relacsed_nix[index_multi_tag]
|
|
||||||
+ 2
|
|
||||||
)
|
|
||||||
]
|
|
||||||
]
|
|
||||||
|
|
||||||
if start_repro_multi_tag.size == 0:
|
relacs_types = [
|
||||||
log.debug("Did not find any peaks for new start multi tag")
|
"relacs.data.sampled.V-1",
|
||||||
log.debug(
|
"relacs.data.sampled.EOD",
|
||||||
f"Differenz to end of repro {end_repro - (positions[-1] + extents_relacsed_nix[index_multi_tag])}"
|
"relacs.data.sampled.LocalEOD-1",
|
||||||
)
|
"relacs.data.sampled.GlobalEFieldStimulus",
|
||||||
break
|
"relacs.data.events.Spikes-1",
|
||||||
|
"relacs.data.events.Chirps",
|
||||||
|
"relacs.data.events.LocalBeat-1-1",
|
||||||
|
]
|
||||||
|
|
||||||
if start_repro_multi_tag.size > 1:
|
efish_group = self.block.create_group("relacs", "relacs.sampled")
|
||||||
if np.all(np.diff(start_repro_multi_tag) > 0.005):
|
|
||||||
log.error("Wrong end point in end of repro")
|
|
||||||
log.error(f"Repro_name: {name[repro_index]}")
|
|
||||||
log.error(f"multitag_index: {index_multi_tag}")
|
|
||||||
log.error(f"max_value {np.max(start_repro_multi_tag)}")
|
|
||||||
exit(1)
|
|
||||||
start_repro_multi_tag = np.mean(start_repro_multi_tag)
|
|
||||||
else:
|
|
||||||
start_repro_multi_tag = start_repro_multi_tag[0]
|
|
||||||
if end_repro - start_repro_multi_tag < 1:
|
|
||||||
log.debug("Posssible endpoint detected")
|
|
||||||
log.debug(
|
|
||||||
f"Differenz to repro end: {end_repro - start_repro_multi_tag}"
|
|
||||||
)
|
|
||||||
break
|
|
||||||
|
|
||||||
positions.append(np.array(start_repro_multi_tag))
|
for i, re in enumerate(relacs):
|
||||||
extents.append(extents_relacsed_nix[index_multi_tag])
|
log.debug(f"Appending relacs efish traces {re}")
|
||||||
|
efish_relacs_data_array = self.relacs_block.data_arrays[re]
|
||||||
positions = np.array(positions).reshape(len(positions), 1)
|
data_array = self.block.create_data_array(
|
||||||
extents = np.array(extents)
|
f"{re}",
|
||||||
if positions.size != extents.size:
|
f"{relacs_types[i]}",
|
||||||
log.error("Calcualted positions and extents do not match ")
|
data=efish_relacs_data_array[:],
|
||||||
log.error(
|
label=efish_relacs_data_array.label,
|
||||||
f"Shape positions {positions.shape}, shape extents {extents.shape}"
|
unit=efish_relacs_data_array.unit,
|
||||||
|
)
|
||||||
|
if efish_relacs_data_array.dimensions[0].dimension_type == nixio.DimensionType.Sample:
|
||||||
|
data_array.append_sampled_dimension(
|
||||||
|
efish_relacs_data_array.dimensions[0].sampling_interval,
|
||||||
|
label="time",
|
||||||
|
unit="s",
|
||||||
)
|
)
|
||||||
if positions.shape != extents.shape:
|
elif efish_relacs_data_array.dimensions[0].dimension_type == nixio.DimensionType.Range:
|
||||||
log.error("Shape of Calculated positions and extents do not match")
|
data_array.append_range_dimension(
|
||||||
log.error(
|
np.sort(efish_relacs_data_array.dimensions[0].ticks),
|
||||||
f"Shape positions {positions.shape}, shape extents {extents.shape}"
|
label="time",
|
||||||
|
unit="s",
|
||||||
)
|
)
|
||||||
embed()
|
|
||||||
exit()
|
|
||||||
|
|
||||||
nix_mtag = self.block.create_multi_tag(
|
efish_group.data_arrays.append(data_array)
|
||||||
f"{nix_group.name}",
|
|
||||||
f"{nix_group.type}",
|
|
||||||
positions=positions,
|
|
||||||
extents=extents,
|
|
||||||
)
|
|
||||||
nix_mtag.metadata = self.nix_file.sections[name]
|
|
||||||
|
|
||||||
# NOTE: adding refs to mtag
|
def append_raw_data(self):
|
||||||
[
|
gr = self.block.create_group("neuronal-data", "open-epyhs.sampled")
|
||||||
nix_mtag.references.extend(ref_groups.data_arrays)
|
raw_neo_data = self.neo_data[0].segments[0].analogsignals[0].load()
|
||||||
for ref_groups in referencs_groups
|
|
||||||
if ref_groups.data_arrays
|
|
||||||
]
|
|
||||||
nix_group.multi_tags.append(nix_mtag)
|
|
||||||
|
|
||||||
def plot_stimulus(self):
|
log.debug("Appending raw data")
|
||||||
ttl_oeph = self.block.data_arrays["ttl-line"][:]
|
nix_data_array = self.block.create_data_array(
|
||||||
|
name="data",
|
||||||
time_index = np.arange(len(ttl_oeph))
|
array_type="open-ephys.data.sampled",
|
||||||
peaks_ttl = time_index[(np.roll(ttl_oeph, 1) < 2) & (ttl_oeph > 2)]
|
dtype=nixio.DataType.Int16,
|
||||||
|
data=raw_neo_data,
|
||||||
stimulus_oeph = self.block.data_arrays["stimulus"]
|
unit="uV",
|
||||||
stimulus = self.relacs_block.data_arrays["GlobalEFieldStimulus"]
|
|
||||||
|
|
||||||
plt.plot(np.arange(stimulus.size) / 20_000.0, stimulus, label="relacs-stimulus")
|
|
||||||
plt.plot(
|
|
||||||
np.arange(len(stimulus_oeph)) / 30_000.0,
|
|
||||||
stimulus_oeph[:],
|
|
||||||
label="open-ephys",
|
|
||||||
)
|
)
|
||||||
plt.plot(
|
nix_data_array.append_sampled_dimension(
|
||||||
np.arange(len(ttl_oeph)) / 30_000.0,
|
1 / raw_neo_data.sampling_rate.magnitude, label="time", unit="s"
|
||||||
ttl_oeph[:],
|
|
||||||
label="ttl-line",
|
|
||||||
)
|
)
|
||||||
plt.scatter(
|
gr.data_arrays.append(nix_data_array)
|
||||||
np.arange(len(ttl_oeph))[peaks_ttl] / 30_000.0,
|
|
||||||
ttl_oeph[peaks_ttl],
|
|
||||||
label="detected peaks",
|
|
||||||
color="red",
|
|
||||||
zorder=100,
|
|
||||||
)
|
|
||||||
plt.legend(loc="upper right")
|
|
||||||
plt.show()
|
|
||||||
|
|
||||||
def close(self):
|
def close(self):
|
||||||
self.dataset.close()
|
|
||||||
self.nix_file.close()
|
self.nix_file.close()
|
||||||
self.relacs_nix_file.close()
|
self.relacs_nix_file.close()
|
||||||
|
|
||||||
|
|
||||||
# if __name__ == "__main__":
|
|
||||||
# create_nix = CreateNix()
|
|
||||||
# create_nix.create_repros_automatically()
|
|
||||||
# create_nix.plot_stimulus()
|
|
||||||
# # create_nix.create_repros_from_config_file()
|
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user