cbica / figuregenerator Goto Github PK

Is your feature request related to a problem? Please describe.
Currently, there is only the default font size, which is fine for most applications, but this requires a bit of optional customization for different layouts.

Describe the solution you'd like
Add a new CLI parameter -fontsize that handles this.

Describe alternatives you've considered
N.A.

Additional context
N.A.

Is your feature request related to a problem? Please describe.
Currently, multiple modalities are displayed as the following:

Coronal_${Modality},         Sagittal_${Modality},         Axial_${Modality}
Coronal_${Modality}_${Mask}, Sagittal_${Modality}_${Mask}, Axial_${Modality}_${Mask}

which is good but it doesn't work well for manuscripts.

Describe the solution you'd like
For manuscript publication, it would be better to have the option to showcase the figure in the following manner:

# first rows contain all images but with each view coming at the same time
Coronal_${Modality_0},         Coronal_${Modality_1},         Sagittal_${Modality_0},         Sagittal_${Modality_1},         Axial_${Modality_0},         Axial_${Modality_1} 
Coronal_${Modality_2},         Coronal_${Modality_3},         Sagittal_${Modality_2},         Sagittal_${Modality_3},         Axial_${Modality_2},         Axial_${Modality_3}

# next rows contain the same view but with mask(s)
Coronal_${Modality_0}_${Mask}, Coronal_${Modality_1}_${Mask}, Sagittal_${Modality_0}_${Mask}, Sagittal_${Modality_1}_${Mask}, Axial_${Modality_0}_${Mask}, Axial_${Modality_1}_${Mask} 
Coronal_${Modality_2}_${Mask}, Coronal_${Modality_3}_${Mask}, Sagittal_${Modality_2}_${Mask}, Sagittal_${Modality_3}_${Mask}, Axial_${Modality_2}_${Mask}, Axial_${Modality_3}_${Mask}

Describe alternatives you've considered
N.A.

Additional context
Feedback from @sbakas from an important manuscript.

Is your feature request related to a problem? Please describe.
Currently, only the x-axis is getting populated, but the y-axis is blank.

Describe the solution you'd like
Adding the files basename in the y-axis would make it much easier to edit as a figure. Or perhaps, adding a string list of labels from the user.

Describe alternatives you've considered
Currently, a user needs to add these titles manually.

Additional context
N.A.

Is your feature request related to a problem? Please describe.
Currently, there is no option for changing the colormap, and adding this option would be nice.

Describe the solution you'd like
Add option to change colormap for better visualization.

Describe alternatives you've considered
N.A.

Additional context

• Look-up table is ready: https://github.com/CBICA/FigureGenerator/blob/main/FigureGenerator/utils.py#L5
• The following option in utils.alpha_blend did not work:

  filter_overlay.SetColormap(sitk.ScalarToRGBColormapImageFilter.Jet)