File Mapping¶

This page provides a complete reference for files that were relocated from the original blech_clust to the current fork.

Root Level to utils/¶

Utility scripts moved from the repository root to utils/:

Original Location	New Location
`clustering.py`	`utils/clustering.py`
`read_file.py`	`utils/read_file.py`
`split_h5_files.py`	`utils/blech_split_h5_files.py`
`blech_waveforms_datashader.py`	`utils/blech_waveforms_datashader.py`
`blech_held_units_detect.py`	`utils/blech_held_units_detect.py`
`blech_hdf5_repack.py`	`utils/blech_hdf5_repack.py`
`blech_nex_convert.py`	`utils/blech_nex_convert.py`
`fix_laser_sampling_errors.py`	`utils/fix_laser_sampling_errors.py`
`memory_monitor.py`	`utils/ram_monitor.py`

Import Changes¶

If you have scripts that imported from the original locations, update your imports:

# Original
from clustering import ...
from read_file import ...

# Current
from utils.clustering import ...
from utils.read_file import ...

EMG Scripts to emg/¶

All EMG-related scripts have been consolidated in the emg/ directory:

Original Location	New Location
`filter_emg.py`	`emg/emg_filter.py`
`emg_local_BSA.py`	`emg/emg_local_BSA_execute.py`
`emg_local_BSA_execute.py`	`emg/emg_local_BSA_execute.py`
`emg_local_BSA_post_process.py`	`emg/emg_freq_post_process.py`
`emg_BSA_segmentation.py`	`emg/emg_freq_setup.py`
`emg_BSA_segmentation_plot.py`	`emg/emg_freq_plot.py`
`get_gapes_Li.py`	`emg/gape_QDA_classifier/get_gapes_Li.py`
`detect_peaks.py`	`emg/gape_QDA_classifier/detect_peaks.py`
`QDA_nostd_no_first.mat`	`emg/gape_QDA_classifier/QDA_nostd_no_first.mat`

Merged Functionality¶

Some EMG scripts were merged or integrated:

Original	Current	Notes
`emg_make_arrays.py`	`blech_make_arrays.py`	EMG array creation integrated into main array generation

Renamed Scripts¶

Some scripts were renamed for clarity or consistency:

Original Name	New Name	Notes
`blech_unit_visualize.py`	`blech_units_plot.py`	Enhanced with additional visualizations
`blech_units_similarity.py`	`utils/qa_utils/unit_similarity.py`	Moved to QA utilities
`memory_monitor.py`	`utils/ram_monitor.py`	Renamed for clarity

New utils/ Structure¶

The utils/ directory contains several new subdirectories:

utils/
├── __init__.py
├── blech_channel_profile.py
├── blech_data_summary.py
├── blech_hdf5_repack.py
├── blech_held_units_detect.py
├── blech_nex_convert.py
├── blech_post_process_utils.py
├── blech_process_utils.py
├── blech_reload_amp_digs.py
├── blech_spike_features.py
├── blech_split_h5_files.py
├── blech_utils.py
├── blech_waveforms_datashader.py
├── cluster_stability.py
├── clustering.py
├── fix_laser_sampling_errors.py
├── grade_dataset.py
├── grading_metrics.json
├── importrhdutilities.py
├── infer_rnn_rates.py
├── makeRaisedCosBasis.py
├── ram_monitor.py
├── read_file.py
├── ephys_data/
│   ├── BAKS.py
│   ├── ephys_data.py
│   ├── lfp_processing.py
│   ├── visualize.py
│   ├── convenience_scripts/
│   └── tests/
├── qa_utils/
│   ├── channel_corr.py
│   ├── drift_check.py
│   ├── elbo_drift.py
│   └── unit_similarity.py
└── umap_plotting/
    ├── bash_umap_parallel.sh
    └── umap_plots.py

New emg/ Structure¶

The emg/ directory organization:

emg/
├── __init__.py
├── emg_filter.py
├── emg_freq_plot.py
├── emg_freq_post_process.py
├── emg_freq_setup.py
├── emg_local_BSA_execute.py
├── emg_local_STFT_execute.py
├── emg_run_pipeline.sh
├── _archive/
│   └── emg_process_comparison.py
├── gape_QDA_classifier/
│   ├── QDA_classifier.py
│   ├── QDA_nostd_no_first.mat
│   ├── detect_peaks.py
│   ├── get_gapes_Li.py
│   └── _experimental/
└── utils/
    └── emg_reload_raw_data.py

Command Line Usage Changes¶

If you were running scripts from the command line, update your paths:

# Original
python filter_emg.py
python get_gapes_Li.py
python blech_held_units_detect.py

# Current
python emg/emg_filter.py
python emg/gape_QDA_classifier/get_gapes_Li.py
python utils/blech_held_units_detect.py

Or use the convenience scripts:

# EMG pipeline
bash emg/emg_run_pipeline.sh /path/to/data

# Main pipeline
bash blech_autosort.sh /path/to/data

Finding Functionality¶

If you're looking for specific functionality from the original codebase:

Looking for...	Now in...
Spike clustering	`utils/clustering.py`
File reading	`utils/read_file.py`, `utils/importrhdutilities.py`
Waveform visualization	`utils/blech_waveforms_datashader.py`
Held unit detection	`utils/blech_held_units_detect.py`
HDF5 operations	`utils/blech_hdf5_repack.py`, `utils/blech_split_h5_files.py`
NEX file conversion	`utils/blech_nex_convert.py`
Memory monitoring	`utils/ram_monitor.py`
EMG filtering	`emg/emg_filter.py`
Gape detection	`emg/gape_QDA_classifier/get_gapes_Li.py`
LFP processing	`utils/ephys_data/lfp_processing.py`
Unit similarity	`utils/qa_utils/unit_similarity.py`
Drift detection	`utils/qa_utils/drift_check.py`
PSTH overlay	`blech_units_characteristics.py`, `utils/ephys_data/`