Removed Features

This page documents components removed from the original blech_clust and their alternatives in the current fork.

Legacy Code

Python 2 Backups

The python2_legacy_code/ directory has been removed. This contained .bak files from the Python 2 to Python 3 migration:

• blech_clust.py.bak
• blech_held_units_detect.py.bak
• blech_multinomial_hmm.py.bak
• blech_palatability_identity_plot.py.bak
• blech_palatability_identity_setup.py.bak
• blech_post_process.py.bak
• blech_process.py.bak
• blech_setup_hmm.py.bak
• blech_units_distance.py.bak
• detect_peaks.py.bak
• emg_BSA_segmentation_plot.py.bak
• emg_local_BSA.py.bak
• emg_local_BSA_post_process.py.bak
• emg_make_arrays.py.bak
• memory_monitor.py.bak
• units_make_arrays.py.bak

Rationale: Python 2 reached end-of-life in 2020. The current codebase is Python 3 only.

Original Entry Point

blech_clust.py has been removed and replaced by a modular pipeline:

Original	Current
blech_clust.py	blech_exp_info.py → blech_init.py → blech_common_avg_reference.py → blech_run_process.sh → ...

The modular approach allows:

• Running individual steps independently
• Better error recovery (restart from failed step)
• Clearer separation of concerns

---

LFP Analysis

The entire LFP_analysis/ directory has been removed:

Removed File	Description
Compare_frequency_envelopes.py	Frequency envelope comparison
GFP_frequency_band_extraction.py	Global field power extraction
LFP_Processing_Final.py	Main LFP processing
LFP_Spectrogram_stone.py	Spectrogram generation
LFP_create_m_file.py	MATLAB file creation
LFP_create_m_file_daniel.py	MATLAB file creation (variant)
LFP_spike_lock_setup_Final.py	Spike-LFP locking setup
Laser_LFP_Parse_Final.py	Laser trial LFP parsing
compare_passive_FRH_dumps.py	Passive firing rate comparison
passive_FRH_grouped.py	Grouped passive firing rates
passive_FRH_grouped_sumchange.py	Summed change analysis
passive_firing_rates.py	Passive firing rate calculation
passive_firing_rates_delta.py	Delta firing rate analysis
_old/ subdirectory	Archived versions

Alternative

LFP functionality is now available through the ephys_data module:

from utils.ephys_data.ephys_data import ephys_data
from utils.ephys_data import lfp_processing

# Load data
data = ephys_data(data_dir='/path/to/data')

# Set LFP parameters
data.lfp_params = {
    'freq_bounds': [1, 300],
    'sampling_rate': 30000,
    'taste_signal_choice': 'Start',
    'fin_sampling_rate': 1000,
    'trial_durations': [2000, 5000]
}

# Extract and load LFPs
data.extract_lfps()
data.get_lfps()
lfp_data = data.lfp_array

See Ephys Data Reference for complete documentation.

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HMM Analysis

Hidden Markov Model analysis scripts have been removed:

Removed File	Description
blech_hmm.py	Basic HMM implementation
blech_multinomial_hmm.py	Multinomial HMM
blech_poisson_hmm.py	Poisson HMM
blech_setup_hmm.py	HMM setup and configuration
variational_HMM_implement.py	Variational HMM implementation
variational_HMM_line_up_palatability_plot.py	Palatability alignment plots
variational_HMM_setup.py	Variational HMM setup

Alternatives

HMM analysis is available in dedicated repositories:

• PyHMM - Original HMM implementation for neural data
• pytau - Updated HMM analysis toolkit

These repositories provide HMM functionality with:

• Dedicated dependencies and environment management
• Active development and maintenance
• Documentation specific to HMM analysis

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Palatability/Identity Analysis

The additional_analyses/ directory has been removed:

Removed File	Description
blech_palatability_identity_plot.py	Palatability/identity visualization
blech_palatability_identity_setup.py	Analysis setup
blech_palatability_regression.py	Regression analysis
blech_hmm_emg_plot.py	HMM-EMG combined plots
blech_identity_palatability_switch.py	Switch point analysis
identity_palatability_switch_EM.py	EM-based switch detection
identity_palatability_switch_EM_correlation_plot.py	Correlation visualization
identity_palatability_switch_EM_implement.py	EM implementation
identity_palatability_switch_correlation_plot.py	Correlation plots
identity_palatability_switch_functions.py	Helper functions
identity_palatability_switch_process.py	Processing pipeline
identity_palatability_switch_setup.py	Setup configuration

Alternative

Basic palatability analysis is available through the ephys_data module:

from utils.ephys_data.ephys_data import ephys_data

data = ephys_data(data_dir='/path/to/data')
data.get_unit_descriptors()
data.get_spikes()
data.get_firing_rates()

# Calculate palatability correlations
data.calc_palatability()

# Access results
pal_df = data.pal_df       # Palatability rankings
pal_array = data.pal_array # Palatability correlations over time

For advanced identity/palatability switch analysis, contact the lab.

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Laser Effect Analysis

The laser_effect_analysis/ directory has been removed:

Removed File	Description
compare_laser_effects.py	Laser effect comparison
laser_effects_plot.py	Laser effect visualization

Alternative

Laser trial separation is available through the ephys_data module:

from utils.ephys_data.ephys_data import ephys_data

data = ephys_data(data_dir='/path/to/data')
data.get_spikes()
data.get_firing_rates()

# Check for laser trials
data.check_laser()

if data.laser_exists:
    # Separate data by laser condition
    data.separate_laser_data()

    # Access separated data
    on_spikes = data.on_spikes
    off_spikes = data.off_spikes
    on_firing = data.on_firing
    off_firing = data.off_firing

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Miscellaneous Removed Files

Examples Directory

The examples/ directory has been removed:

Removed	Description
Half-Gaussian PSTH example.ipynb	Jupyter notebook example

Example usage is now documented in the Tutorials and API reference pages.

Root-Level Scripts

Several root-level scripts have been removed or relocated:

Removed	Status
blech_dat_file_join.py	Functionality integrated into data loading
overlay_psth.py	Functionality in blech_units_characteristics.py and ephys_data module

See File Mapping for scripts that were relocated rather than removed.