Cli Tac Fitting#

Command-line interface (CLI) for fitting Tissue Compartment Models (TCM) to PET Time-Activity Curves (TACs).

This module provides a CLI to interact with the tac_fitting module. It utilizes argparse to handle command-line arguments.

The user must provide:

  • Input TAC file path

  • Region of Interest (ROI) TAC file path

  • Compartment model name for fitting. Supported models are ‘1tcm’, ‘2tcm-k4zero’, or ‘serial-2tcm’.

  • Filename prefix for the output files

  • Output directory where the analysis results will be saved

  • Whether to ignore blood volume contributions while fitting

  • Threshold in minutes (input fitting threshold)

User can optionally provide:

  • Initial guesses for the fitting parameters

  • Lower and upper bounds for the fitting parameters

  • Maximum number of function iterations

  • Decay constant (in minutes) for per-frame weighting

This script utilizes the TCMAnalysis class to perform the TAC fitting and save

the results accordingly.

Examples

In the proceeding example, we assume that we have an input TAC named ‘input_tac.txt’, and an ROI TAC named ‘roi_tac.tsv’. We want to try fitting a serial 2TCM to the ROI tac.

petpal-tcm-fit interp -i "input_tac.tsv"\
-r "roi_tac.tsv"\
-m "serial-2tcm"\
-o "./" -p "cli_"\
-t 35.0\
-g 0.1 0.1 0.1 0.1 0.1\
-l 0.0 0.0 0.0 0.0 0.0\
-u 5.0 5.0 5.0 5.0 5.0\
-f 2500 -n 4096 -b --print
In this next example, we assume that we have an input TAC named ‘input_tac.txt’, an ROI TACs directory

named ‘./roi_tas/’ which contains TACs for different ROIs, and a scan/image metadata file called ‘scan_info.json’. We want to try fitting serial 2TCM to the ROI tacs, with the default bounds.

petpal-tcm-fit frame_avgd -i "input_tac.tsv"\
-r "./roi_tacs/"\
-s "scan_info.json"\
-m "serial-2tcm"\
-o "./" -p "cli_"\
-f 2500 -n 4096 -b --print

See also

petpal.tac_fitting - module for fitting TACs with TCMs.

Attributes#

_EXAMPLE_

Functions#

add_common_io_args(→ argparse._ArgumentGroup)

Adds common input/output arguments to the provided argument parser.

add_common_analysis_args(parser)

Adds common analysis-related arguments to the provided argument parser.

add_common_print_args(parser)

Adds common verbosity/printing arguments to the provided argument parser.

_generate_args(→ argparse.Namespace)

Generates and handles the arguments for the command-line interface.

_generate_bounds(→ Union[numpy.ndarray, None])

Generates the bounds for the fitting parameters.

fit_props_printer(→ None)

Nicely formats and prints fit parameter estimates and uncertainties.

Module Contents#

petpal.cli.cli_tac_fitting._EXAMPLE_ = Multiline-String#
Show Value
"""Fitting a TAC to the serial 2TCM using the interpolation strategy:
  petpal-tcm-fit interp -i "input_tac.txt" -r "2tcm_tac.txt" -m "serial-2tcm" -o "./" -p "cli_" -t 35.0 -g 0.1 0.1 0.1 0.1 0.1 -l 0.0 0.0 0.0 0.0 0.0 -u 5.0 5.0 5.0 5.0 5.0 -f 2500 -n 4096 -b --print

Fitting a TAC to the serial 2TCM using the frame averaged strategy:
  petpal-tcm-fit frame_avgd -i "input_tac.txt" -r "2tcm_tac.txt" -s scan_metadata.json -m "serial-2tcm" -o "./" -p "cli_" -g 0.1 0.1 0.1 0.1 0.1 -l 0.0 0.0 0.0 0.0 0.0 -u 5.0 5.0 5.0 5.0 5.0 -f 2500 -n 4096 -b --print"""