arista.ingest.parsers.robert
Walk Robert Kossen’s Compiled_data_pickled/<genotype>/*.txt tree.
Each TXT carries a five-line #-prefixed provenance header followed
by a whitespace-separated 3-column body:
# date: 2018-02-07
# genotype: CantonS
# gender: m01
# stimulus: ascAmp
# celltype: CC
0 21.47 -0.004010
1 21.47 0.001740
…
Filenames follow YYYY-MM-DD_<strain>_<sex><animal_num>[suffix]_<stim>_<cell>_<n>.txt;
the per-file gender header field packs sex + animal-of-the-day +
optional b-for-second-arista into one string (“m01”, “f02b”, …).
The dfbf column in the TXT is the canonical post-pipeline ΔF/F₀
(drift-corrected per the pytci massiveAligner workflow). Robert’s
TXT export dropped the original choice of fit method so
recordings.drift_correction = 'unknown' and the raw pre-correction
trace is not recoverable from the TXT alone. We store the TXT value
in samples.dfbf and leave samples.dfbf_drift_corrected NULL —
the column represents “raw fed in vs corrected from raw”; we lack
the raw side.
Niko’s 2016 recordings were re-processed through this same pipeline
and live in NSybLexALexOpGCamp6/, so they are also ingested via
this parser, attributed to the same researcher as the rest of the
compiled tree.
Module Attributes
Default sample rate. |
Functions
|
Yield one |
- arista.ingest.parsers.robert.DEFAULT_FPS = 10.0
Default sample rate. Robert’s pipeline assumed 10 fps throughout the corpus; the TXT carries no per-file fps so we hard-code.
- arista.ingest.parsers.robert.discover_robert_records(source_root)[source]
Yield one
DiscoveryResultper TXT underCompiled_data_pickled/.The expected tree is
<source_root>/<genotype>/*.txtwhere<genotype>is one of CantonS / NompC3_NSybLexALexOpGCamp6 / NompC-HeterozControl / NompCPbac / NompCRescue / NompCOverExpression / NompCGal4-Ctrl-NCBG / NompCGal4-Ctrl-WTBG / UASNompC-Ctrl-NCBG / NSybLexALexOpGCamp6 / ColdAdapt / HotAdapt / AristaBending.Files outside that pattern are yielded with
record=Noneand a populatedreasonso the CLI surface can show them.- Parameters:
source_root (Path) – Path to
Compiled_data_pickled/(or an equivalent tree of<genotype>/<txt>).- Return type: