cmind.utils.image_utils

Image Utilities A series of utilities for working with images (.gif, .png, etc)

Functions

ImageMagick_append_label(input_image, ...[, ...]) Append a label to the top, bottom, right or left of an image
ImageMagick_build_colorbar(output_img[, ...]) Append a label to the top, bottom, right or left of an image
ImageMagick_crop_border(input_image[, ...]) Trim borders from an image
ImageMagick_get_size(image_file) Returns size of an image as [width,height]
ImageMagick_resize(input_image, pct[, ...]) Resize an image
cmind_dual_func_overlay(bg_image, ...[, ...]) utility to overlay both positive and negative activations on a single
designmat_plot(dm[, col_width_pixels, ...])
mpl_white_on_black(f) convert matplotlib figure to white text on black bacground
random_color_str([cmin, cmax]) return a randomized RGB hex color string “#{RRGGBB}” for use in a graphviz .dot file.
set_backgroundcolor(ax, color) Sets the background color of the current axes (and legend).
set_foregroundcolor(ax, color) For the specified axes, sets the color of the frame, major ticks,
slicer_3plane_fig(input_volume[, istr, ...]) Use FSL’s slicer to generate a center slice in each image plane
slicer_mid_sag_fig(input_volume[, istr, ...]) Use FSL’s slicer to generate a mid-sagittal image
slicer_tile_slices(input_volume[, ...]) Use FSL’s slicer to create a mosaic of axial images
cmind.utils.image_utils.slicer_3plane_fig(input_volume, istr='', output_image=None, verbose=False, logger=None)[source]

Use FSL’s slicer to generate a center slice in each image plane

Parameters:

input_volume : str

filename of input volume

istr : str, optional

optional string containing additional command line arguments

output_image : str, optional

override default filename for output image with this one

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

Returns:

output_image : str

filename of the generated image

cmind.utils.image_utils.slicer_mid_sag_fig(input_volume, istr='', output_image=None, verbose=False, logger=None)[source]

Use FSL’s slicer to generate a mid-sagittal image

Parameters:

input_volume : str

filename of input volume

istr : str, optional

optional string containing additional command line arguments

output_image : str, optional

override default filename for output image with this one

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

Returns:

output_image : str

filename of the generated image

cmind.utils.image_utils.slicer_tile_slices(input_volume, optional_args='', slice_skip=1, width=800, output_image=None, verbose=False, logger=None)[source]

Use FSL’s slicer to create a mosaic of axial images

Parameters:

input_volume : str

filename of input volume

optional_args : str, optional

optional string containing additional command line arguments

slice_skip : int, optional

slice skip factor

width : int, optional

width of the mosaic in pixels

output_image : str, optional

override default filename for output image with this one

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

Returns:

output_image : str

filename of the generated image

cmind.utils.image_utils.ImageMagick_get_size(image_file)[source]

Returns size of an image as [width,height]

Parameters:

image_file : str

image file to query

Returns:

size_list : list

[width, height] as floats

cmind.utils.image_utils.ImageMagick_build_colorbar(output_img, cbar_input_img=None, cbar_label=['low', 'high'], rotate_cbar_img=0, vertical_cbar=False, cbar_input_resize_pct=200, bg_color='black', text_color='white', pointsize=None, verbose=False, logger=None)[source]

Append a label to the top, bottom, right or left of an image

Parameters:

output_img : str

output filename for the colorbar image

cbar_input_img : str

filename of the colorbar image (without labels)

cbar_label : str, optional

2-element list corresponding to the labels for the (low,high) ends of the colorbar

rotate_cbar_img : float, optional

if > 0, the colorbar image will be rotated by this amount

vertical_cbar : bool, optional

if true, the colorbar labels will be stacks above/below the colorbar instead of left/right

cbar_input_resize_pct : int, optional

percentage by which to resize cbar_input_img

bg_color : str, optional

color of the label background

text_color : str, optional

color of the label text

pointsize : int, optional

pointsize of the label text. If unspecified, will match size of the colorbar

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

cmind.utils.image_utils.ImageMagick_crop_border(input_image, output_image=None, verbose=False, logger=None)[source]

Trim borders from an image

Parameters:

input_image : str

filename for the input image

output_image : str, optional

filename for the output image

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

cmind.utils.image_utils.ImageMagick_append_label(input_image, title_string, output_image=None, position='top', bg_color='black', text_color='white', pointsize=90, colorspace='sRGB', verbose=False, logger=None)[source]

Append a label to the top, bottom, right or left of an image

Parameters:

input_image : str

filename for the input image

label_string : str

text for the label

output_image : str, optional

filename for the output image

bg_color : str, optional

color of the label background

text_color : str, optional

color of the label text

position : str, {‘top’,’bottom’,’left’,’right’}

controls the position or the label. If ‘left’ or ‘right’ label text will run vertically.

pointsize : int, optional

pointsize of the label text

colorspace : str, optional

modify colorspace of image. default = sRGB

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

cmind.utils.image_utils.random_color_str(cmin=0, cmax=14737632)[source]

return a randomized RGB hex color string “#{RRGGBB}” for use in a graphviz .dot file.

Parameters:

cmin : int, optional

minimum allowed RGB color: must be in range [0x00000 0xffffff] (R, G, B can each range from 0x00 to 0xff corresponding to the integer range [0 255])

cmax : int, optional

maximum allowed color: must be in range [0x00000 0xffffff]

Returns:

color_code : str

color code string for use in graphviz .dot files