essfile 0.3.3

Reader and analysis tools for dserv ESS experiment log files

essfile

Pure Python reader and analysis tools for dserv ESS experiment log files.

Installation

pip install essfile

This installs essfile with numpy and dgread (for stimulus parameter decoding).

For pandas DataFrame support:

pip install essfile[pandas]

Quick Start

Inspect an ESS file from the command line

essread session.ess
essread session.ess --raw   # show flat datapoint stream

Read in Python

from essfile import ESSFile

f = ESSFile('session.ess')
print(f.identity)    # {'ess': 'hapticvis', 'subject': 'human', ...}
print(f.params)      # {'stim_duration': '30000', ...}
print(f.n_obs)       # 12
print(f.stimdg)      # dict of numpy arrays (stimulus parameters)

Extract trials

from essfile import ESSFile
from essfile.extract.hapticvis import extract_trials

f = ESSFile('session.ess')
trials = extract_trials(f)

print(trials['rt'])       # reaction times
print(trials['correct'])  # 0/1 accuracy

# Convert to DataFrame
import pandas as pd
df = pd.DataFrame(trials)

Low-level access

from essfile import read_dslog, read_ess

# Flat datapoint stream (varname, timestamp, vals columns)
d = read_dslog('session.ess')

# Obs-period oriented with parsed preamble
ess = read_ess('session.ess')

Architecture

The package has three layers:

Layer	Function	Description
essread	read_dslog()	Binary parser → flat datapoint stream
essread	read_ess()	Segments into obs periods, parses preamble
essfile	ESSFile	Event query API (select, sparse, nested)
extract.*	extract_trials()	System-specific trial extraction

ESSFile API

The ESSFile class provides methods matching the Tcl df::File API:

f = ESSFile('session.ess')

# Event selection (returns list of bool arrays, one per obs)
mask = f.select_evt('ENDTRIAL')
mask = f.select_evt('STIMULUS', 'ON')

# Sparse extraction (one value per trial, fill=-1 if missing)
valid = np.where(some_condition)[0]
times = f.event_time_sparse(valid, 'RESP')
params = f.event_param_sparse(valid, 'STIMTYPE')
subtypes = f.event_subtype_sparse(valid, 'ENDTRIAL')

# Nested extraction (variable count per trial)
decide_times = f.event_times_nested(valid, 'DECIDE', 'SELECT')

# Name lookups
f.type_id('ENDTRIAL')                    # -> 40
f.subtype_id('ENDTRIAL', 'CORRECT')      # -> 1
f.has_event_type('CHOICES')               # -> True

Writing Extractors

System-specific extractors live in essfile.extract. Each provides an extract_trials(f) function that takes an ESSFile and returns a dict of equal-length arrays (one entry per valid trial).

See essfile/extract/hapticvis.py for a complete example.

File Format

ESS files use the dslog binary format produced by dserv's logger:

• 16-byte header: magic dslog, version, timestamp
• Sequence of datapoint records: varname, timestamp, type, data
• Events encoded with type/subtype/puttype in a 4-byte union
• Pre-obs preamble contains event name tables, parameters, stimdg

Requirements

• Python ≥ 3.9
• numpy
• dgread (for stimulus parameter decoding)
• pandas (optional, for DataFrame conversion)

License

MIT