Pre-processing data tool for NHP Lab @ CMU
Project description
nhp-prep
This is a CLI Tool that has been created to pre-process historical data that has been collected in multiple instances. This includes data collected at Seneca Zoo and Mellon Institute.
Requirements
This package requires Python 3.
Installing
To install this CLI tool you can run the below command
pip3 install nhp-prep
Alternatively, you clone this repo and then run this command from within the repository folder
python3 setup.py install
Another way to install this solution is by running the following command from within the repository folder:
pip install -e .
Both the above commands would install the package globally and nhp-prep
will be available on your system.
How to use
There are multiple instances in which you can use this tool.
nhp-prep COMMAND [OPTIONS]
There are four use-cases (commands) in which you can use this tool:
- Mapping columns from prior to current format (
reorder-columns
)
nhp-prep reorder-columns -i <directory_with_files_to_reorder_columns_OR_unique_CSV_file> -o <output_directory> -r <file_with_reference_columns>
- Rename the files to follow current standard (
rename
)
nhp-prep rename -i <directory_files_to_rename_OR_uniques_CSV_file> -o <output_directory>
The current format for the file is: YYYY-MM-DD_HHmmh_<experiment_name>_<Subject_name>_<Researcher_name_or_initials>_data.csv
- Timestamp estimation trials from historical data files based on column (
timestamp-estimate
)
nhp-prep --timestamp-estimate -i <input_file>
Alternatively, you can pass the directory of the files to estimate the timestamp of each trial:
nhp-prep timestamp-estimate -i <directory_with_files_OR_unique_CSV_file>
- Renaming of Subject according to logs file (needs the file) (
sub-rename
)
nhp-prep sub-rename -r <file_with_columns_and_reference_subject_names> -i <directory_with_files_OR_unique_CSV_file> -o <output_directory>
You could also run nhp-prep --help
to see the available commands and their corresponding usage.
If you want to know all the options available for an specific command, run the following:
nhp-prep COMMAND --help
Example:
nhp-prep sub-rename --help
Feedback
Please feel free to leave feedback in issues/PRs.
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