RegionalTacFigure#

class petpal.visualizations.tac_plots.RegionalTacFigure(tacs_dir: str, figsize: tuple = (8, 4), xlabel: str = '$t$ [minutes]', ylabel: str = 'TAC [$\\mathrm{kBq/ml}$]', plot_type='both')#

Bases: TacFigure, petpal.utils.time_activity_curve.MultiTACAnalysisMixin

Handle plotting regional TACs generated with PETPAL. Used when visualizing activity in several brain regions in the same participant, especially after running PETPAL’s write_tacs() or Sgtm methods.

Example:

from petpal.visualizations.tac_plots import RegionalTacFigure
from petpal.utils.time_activity_curve import TimeActivityCurve

## Load up an individual TAC file
my_tac = TimeActivityCurve.from_tsv("/path/to/tac.tsv")

## Select a list of regions to plot and the folder containing TAC files for those regions
my_regions = ['Putamen', 'Cerebellum', 'CorticalGrayMatter']
my_fig = tac_plots.RegionalTacFigure(tacs_dir="/path/to/tacs/folder/")

## Add the individual TAC and the regional TACs to the figure
my_fig.add_errorbar(*my_tac.tac_werr, label='Whole Brain')
my_fig.plot_tacs_in_regions_list(regions=my_regions)

## Write the figure to file
my_fig.write_fig(out_fig_path="/path/to/plot.png")

plt.show() # Comment this out if you don't want to see the figure
# plt.close() # Uncomment this if you don't want to see the figure

Initialize the TacFigure with two subplots, one with a linear scale and the other with a semi-logarithmic scale.

Parameters:

  • figsize (tuple) – The total size of the figure. Defaults to an 8x4 inches figure.

  • xlabel (str) – The label for the x-axis. Defaults to ‘$t$ [minutes]’.

  • ylabel (str) – The label for the y-axis. Defaults to ‘TAC [$mathrm{kBq/ml}$]’.

  • plot_type (str) – Type of plot, with options ‘linear’, ‘log’, or ‘both’.

property tacs_objects_dict#

A dictionary containing region name/TAC object pairs for all TAC files found in tacs_dir.

plot_tacs_in_regions_list(regions: list[str], show_legend: bool = True, colormap: str = 'Dark2', **kwargs)#

Plot TACs for a list of provided regions without errorbars.

Region names correspond to abbreviated segment names in the dseg file used to generate the regions.

Parameters:

  • regions (list[str]) – A list of region names whose TACs are plotted.

  • show_legend (bool) – Show the legend with region names in the resulting figure. Default True.

  • colormap (str) – A matplotlib color map used to select colors of different TAC plots. Default ‘Dark2’.

  • kwargs (dict) – Additional keyword arguments for the plt.plot() function.

plot_tacs_in_regions_list_with_errorbar(regions: list[str], show_legend: bool = True, colormap: str = 'Dark2', **kwargs)#

Plot TACs for a list of provided regions with errorbars.

Region names correspond to abbreviated segment names in the dseg file used to generate the regions.

Parameters:

  • regions (list[str]) – A list of region names whose TACs are plotted.

  • show_legend (bool) – Show the legend with region names in the resulting figure. Default True.

  • colormap (str) – A matplotlib color map used to select colors of different TAC plots. Default ‘Dark2’.

  • kwargs (dict) – Additional keyword arguments for the plt.errorbar() function.

plot_all_regional_tacs(show_legend: bool = True, colormap='Dark2', **kwargs)#

Plot TACs for all TACs found in a folder without errorbars.

Region names correspond to abbreviated segment names in the dseg file used to generate the regions.

Parameters:

  • show_legend (bool) – Show the legend with region names in the resulting figure. Default True.

  • colormap (str) – A matplotlib color map used to select colors of different TAC plots. Default ‘Dark2’.

  • kwargs (dict) – Additional keyword arguments for the plt.plot() function.

plot_all_regional_tacs_with_errorbar(show_legend: bool = True, colormap='Dark2', **kwargs)#

Plot TACs for all TACs found in a folder with errorbars.

Region names correspond to abbreviated segment names in the dseg file used to generate the regions.

Parameters:

  • show_legend (bool) – Show the legend with region names in the resulting figure. Default True.

  • colormap (str) – A matplotlib color map used to select colors of different TAC plots. Default ‘Dark2’.

  • kwargs (dict) – Additional keyword arguments for the plt.errorbar() function.

setup_linear_subplot(xlabel: str, ylabel: str, figsize: tuple)#

Get the figure and axes objects for a 1x1 MatPlotLib subplot.

Parameters:

  • xlabel (str) – The label for the x-axis.

  • ylabel (str) – The label for the y-axis.

  • figsize (tuple) – Size of the figure.

setup_log_subplot(xlabel: str, ylabel: str, figsize: tuple)#

Get the figure and axes objects for a 1x1 MatPlotLib subplot.

Parameters:

  • xlabel (str) – The label for the x-axis.

  • ylabel (str) – The label for the y-axis.

  • figsize (tuple) – Size of the figure.

setup_linear_and_log_subplot(xlabel: str, ylabel: str, figsize: tuple)#

Get the figure and axes objects for a 1x2 MatPlotLib subplot.

Parameters:

  • xlabel (str) – The label for the x-axis.

  • ylabel (str) – The label for the y-axis.

  • figsize (tuple) – Size of the figure.

add_tac(tac_times: numpy.ndarray, tac_vals: numpy.ndarray, **kwargs)#

Add a TAC to both subplots.

Parameters:

  • tac_times (np.ndarray) – The time points for the TAC.

  • tac_vals (np.ndarray) – The corresponding values for the TAC.

  • kwargs (dict) – Additional keyword arguments for the plot() function.

add_errorbar(tac_times: numpy.ndarray, tac_vals: numpy.ndarray, uncertainty: numpy.ndarray, **kwargs)#

Add a lineplot with errorbars to the figure.

Parameters:

  • tac_times (np.ndarray) – Array containing times at which TAC is sampled.

  • tac_vals (np.ndarray) – Array containing TAC activity concentration.

  • uncertainty (np.ndarray) – Array containing uncertainties in TAC measurements.

  • kwargs (dict) – Additional keyword arguments for the plt.errorbar() function.

set_ylim_min_to_zero(**kwargs)#

Set the y-axis lower limit to zero.

Parameters:

kwargs (dict) – Additional keyword arguments for the set_ylim() function.

gen_legend()#

Generate a legend using the labels provided in the add_tac() method.

Note

It is recommended to add all TACs before generating the legend. Any TACs added after

the legend is generated will not be included in the legend.

write_fig(out_fig_path: str, **kwargs)#

Write the figure to a common image file type, such as .png or .jpg. Applies plt.savefig() to figure object.

Parameters:

  • out_fig_path (str) – Path to the file the figure will be written to.

  • kwargs (dict) – Additional key word arguments passed to plt.savefig()

property input_tac_path#

Gets the input TAC file path.

property tacs_dir#

Gets the TAC directory path.

property reference_tac_path#

Gets the reference TAC file path.

is_valid_tacs_dir(tacs_dir: str)#

Validates the TAC directory by checking for TAC files.

Parameters:

tacs_dir (str) – Directory to validate.

Returns:

bool – True if valid, otherwise False.

static get_tacs_list_from_dir(tacs_dir: str) → list[str]#

Retrieves a sorted list of TAC file paths from a directory.

Parameters:

tacs_dir (str) – Directory from which to retrieve TAC files.

Returns:

list[str] – Sorted list of TAC file paths.

static get_tacs_objects_dict_from_files_list(tacs_files_list: list[str])#

Creates a dict of TAC objects from a list of file paths.

Parameters:

tacs_files_list (list[str]) – List of TAC file paths.

Returns:

dict – Dictionary of region name-TAC object pairs.

static get_tacs_objects_dict_from_dir(tacs_dir: str) → dict#

Creates a dict of TAC objects from a directory of TAC files.

Parameters:

tacs_dir (str) – A directory of TAC files.

Returns:

dict – Dictionary of region name-TAC object pairs.

static get_tacs_objects_list_from_files_list(tacs_files_list: list[str])#

Creates a list of TAC objects from a list of file paths.

Parameters:

tacs_files_list (list[str]) – List of TAC file paths.

Returns:

list[TimeActivityCurve] – List of TAC objects.

static get_tacs_vals_from_objs_list(tacs_objects_list: list[TimeActivityCurve])#

Extracts TAC values from a list of TAC objects.

Parameters:

tacs_objects_list (list[TimeActivityCurve]) – List of TAC objects.

Returns:

list – List of TAC values.

get_tacs_vals_from_dir(tacs_dir: str)#

Retrieves TAC values from files in a specified directory.

Parameters:

tacs_dir (str) – Directory containing TAC files.

Returns:

list – List of TAC values.

static capitalize_first_char_of_str(input_str: str)#

Capitalize only the first character of a string, leaving the remainder unchanged.

Parameters:

input_str (str) – The string to capitalize the first character of.

Returns:

output_str (str) – The string with only the first character capitalized.

static infer_segmentation_label_from_tac_path(tac_path: str, tac_id: int)#

Infers a segmentation label from a TAC file path by analyzing the filename.

This method extracts a segment label from the filename of a TAC file. It checks the presence of a seg- marker in the filename, which is followed by the segment name. This segment name is then formatted with each part capitalized. If no segment label is found, a default unknown label is generated using the TAC’s ID.

Parameters:

  • tac_path (str) – Path of the TAC file.

  • tac_id (int) – ID of the TAC.

Returns:

str – Inferred segmentation label.

infer_segmentation_labels_for_tacs()#

Infers segmentation labels for TACs.

Returns:

list[str] – List of inferred segmentation labels.

See also

infer_segmentation_label_from_tac_path()