pybraincompare.compare package

Submodules

pybraincompare.compare.atlas module

atlas.py: part of pybraincompare package Functions to integrate atlases in image comparison

class pybraincompare.compare.atlas.atlas(atlas_xml, atlas_file, views=['axial', 'sagittal', 'coronal'])[source]
get_region_names()[source]
get_static_svg()[source]
make_color_lookup(new_colors)[source]
make_svg(views)[source]
read_xml(atlas_xml)[source]
remove_attributes(path, attributes)[source]
save_svg(output_folder, views=None)[source]
set_attributes(path, attributes, new_values)[source]
class pybraincompare.compare.atlas.region(label, index, x, y, z)[source]

pybraincompare.compare.maths module

maths.py: part of pybraincompare package Simple math functions

pybraincompare.compare.maths.calc_rows_columns(ratio, n_images)[source]
pybraincompare.compare.maths.calculate_atlas_correlation(image_vector1, image_vector2, atlas_vector, atlas_labels, atlas_colors, corr_type='pearson', summary=False)[source]
pybraincompare.compare.maths.calculate_correlation(images, mask=None, atlas=None, summary=False, corr_type='pearson')[source]
pybraincompare.compare.maths.calculate_pairwise_correlation(image_vector1, image_vector2, corr_type='pearson', atlas_vector=None)[source]
pybraincompare.compare.maths.do_multi_correlation(image_df, corr_type='pearson')[source]
pybraincompare.compare.maths.percent_to_float(x)[source]

pybraincompare.compare.mrutils module

mrutils.py: part of pybraincompare package Functions work with brain maps

pybraincompare.compare.mrutils.apply_threshold(image1, thresh, direction='posneg')[source]
pybraincompare.compare.mrutils.do_mask(images, mask)[source]
pybraincompare.compare.mrutils.generate_thresholds(lower=0, upper=4, by=0.01)[source]
pybraincompare.compare.mrutils.get_nii_obj(images)[source]
pybraincompare.compare.mrutils.get_standard_brain(software)[source]
pybraincompare.compare.mrutils.get_standard_mask(software)[source]
pybraincompare.compare.mrutils.get_standard_mat(software)[source]
pybraincompare.compare.mrutils.make_binary_deletion_mask(images)[source]
pybraincompare.compare.mrutils.make_binary_deletion_vector(image_vectors)[source]
pybraincompare.compare.mrutils.make_in_out_mask(mask_bin, mr_folder, masked_in, masked_out, img_dir, save_png=True)[source]
pybraincompare.compare.mrutils.resample_images_ref(images, reference, interpolation, resample_dim=None)[source]
pybraincompare.compare.mrutils.squeeze_fourth_dimension(images)[source]

pybraincompare.compare.network module

network.py: part of pybraincompare package Functions for visualization of functional MRI

pybraincompare.compare.network.connectogram(matrix_file, groups, threshold, network_names=None)[source]

pybraincompare.compare.scatterplot module

scatterplot.py: part of pybraincompare package Functions to perform and create scatterplot comparisons

pybraincompare.compare.scatterplot.get_atlas_objects(atlas, atlas_rendering)[source]
pybraincompare.compare.scatterplot.make_scatterplot_interface(corr_df, elements, error=None, remove_scripts=None)[source]
pybraincompare.compare.scatterplot.scatterplot_canvas(image_vector1, image_vector2, image_names, atlas_vector, atlas_labels, atlas_colors, output_directory, view=True)[source]
pybraincompare.compare.scatterplot.scatterplot_compare(images, image_names, software='FSL', atlas=None, atlas_rendering=None, custom=None, corr_type='pearson', reference=None, resample_dim=[8, 8, 8], remove_scripts=None, width=1200)[source]
pybraincompare.compare.scatterplot.scatterplot_compare_error(template, specific_error)[source]
pybraincompare.compare.scatterplot.scatterplot_compare_vector(image_vector1, image_vector2, image_names, atlas_vector, atlas_labels, atlas_colors, custom=None, corr_type='pearson', atlas=None, subsample_every=None, remove_scripts=None, summary=False, width=1200)[source]

pybraincompare.compare.search module

search.py: part of pybraincompare package Generate search interfaces to compare images

calculate_similarity_search_df starts with pandas data frame to make similarity interface

pybraincompare.compare.search.create_glassbrain_portfolio(image_paths, all_tags, unique_tags, placeholders, values=None, button_urls=None, image_urls=None, top_text=None, bottom_text=None)[source]

Module contents