herBAR

A barcode renamer for herbarium specimens

Requirements

Python 3.*

Pillow >= 7.0.0

zbar

pyzbar >= 0.1.9

tqdm >= 4.64.0

Installation

Download the script file to your local computer and install the required modules. To install modules, use pip:

pip install -r requirements.txt

Usage

usage: herbar.py [-h] -s SOURCE [-p {TX,ANHC,VDB,TEST,Ferns,TORCH,EF}]
             [-d DEFAULT_PREFIX] [-b BATCH] [-o [OUTPUT]] [-n] [-c CODE]
             [-v] [-j [JPEG_RENAME]]

optional arguments:
-h, --help            show this help message and exit
-s SOURCE, --source SOURCE
                    Path to the directory that contains the images to be
                    analyzed.
-p {TX,ANHC,VDB,TEST,Ferns,TORCH,EF}, --project {TX,ANHC,VDB,TEST,Ferns,TORCH,EF}
                    Project name for filtering in database
-d DEFAULT_PREFIX, --default_prefix DEFAULT_PREFIX
                    Barcode prefix string which will be used as the
                    primary barcode when multiple barcodes are found.
                    Suppresses multiple barcode names in filename.
-b BATCH, --batch BATCH
                    Flags written to batch_flags, can be used for
                    filtering downstream data.
-o [OUTPUT], --output [OUTPUT]
                    Path to the directory where log file is written. By
                    default (no -o switch used) log will be written to
                    location of script. If just the -o switch is used, log
                    is written to directory indicated in source argument.
                    An absolute or relative path may also be provided.
-n, --no_rename       Files will not be renamed, only log file generated.
-c CODE, --code CODE  Collection or herbarium code prepended to barcode
                    values.
-v, --verbose         Detailed output for each file processed.
-j [JPEG_RENAME], --jpeg_rename [JPEG_RENAME]
                    String will be added to JPEG file names to prevent
                    name conflicts downstream.