pybraincompare.compare package
Submodules
pybraincompare.compare.atlas module
atlas.py: part of pybraincompare package
Functions to integrate atlases in image comparison
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class
pybraincompare.compare.atlas.
atlas
(atlas_xml, atlas_file, views=['axial', 'sagittal', 'coronal'])[source]
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get_region_names
()[source]
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get_static_svg
()[source]
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make_color_lookup
(new_colors)[source]
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make_svg
(views)[source]
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read_xml
(atlas_xml)[source]
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remove_attributes
(path, attributes)[source]
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save_svg
(output_folder, views=None)[source]
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set_attributes
(path, attributes, new_values)[source]
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class
pybraincompare.compare.atlas.
region
(label, index, x, y, z)[source]
pybraincompare.compare.maths module
maths.py: part of pybraincompare package
Simple math functions
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pybraincompare.compare.maths.
calc_rows_columns
(ratio, n_images)[source]
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pybraincompare.compare.maths.
calculate_atlas_correlation
(image_vector1, image_vector2, atlas_vector, atlas_labels, atlas_colors, corr_type='pearson', summary=False)[source]
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pybraincompare.compare.maths.
calculate_correlation
(images, mask=None, atlas=None, summary=False, corr_type='pearson')[source]
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pybraincompare.compare.maths.
calculate_pairwise_correlation
(image_vector1, image_vector2, corr_type='pearson', atlas_vector=None)[source]
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pybraincompare.compare.maths.
do_multi_correlation
(image_df, corr_type='pearson')[source]
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pybraincompare.compare.maths.
percent_to_float
(x)[source]
pybraincompare.compare.mrutils module
mrutils.py: part of pybraincompare package
Functions work with brain maps
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pybraincompare.compare.mrutils.
apply_threshold
(image1, thresh, direction='posneg')[source]
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pybraincompare.compare.mrutils.
do_mask
(images, mask)[source]
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pybraincompare.compare.mrutils.
generate_thresholds
(lower=0, upper=4, by=0.01)[source]
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pybraincompare.compare.mrutils.
get_nii_obj
(images)[source]
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pybraincompare.compare.mrutils.
get_standard_brain
(software)[source]
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pybraincompare.compare.mrutils.
get_standard_mask
(software)[source]
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pybraincompare.compare.mrutils.
get_standard_mat
(software)[source]
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pybraincompare.compare.mrutils.
make_binary_deletion_mask
(images)[source]
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pybraincompare.compare.mrutils.
make_binary_deletion_vector
(image_vectors)[source]
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pybraincompare.compare.mrutils.
make_in_out_mask
(mask_bin, mr_folder, masked_in, masked_out, img_dir, save_png=True)[source]
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pybraincompare.compare.mrutils.
resample_images_ref
(images, reference, interpolation, resample_dim=None)[source]
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pybraincompare.compare.mrutils.
squeeze_fourth_dimension
(images)[source]
pybraincompare.compare.network module
network.py: part of pybraincompare package
Functions for visualization of functional MRI
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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
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pybraincompare.compare.scatterplot.
get_atlas_objects
(atlas, atlas_rendering)[source]
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pybraincompare.compare.scatterplot.
make_scatterplot_interface
(corr_df, elements, error=None, remove_scripts=None)[source]
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pybraincompare.compare.scatterplot.
scatterplot_canvas
(image_vector1, image_vector2, image_names, atlas_vector, atlas_labels, atlas_colors, output_directory, view=True)[source]
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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]
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pybraincompare.compare.scatterplot.
scatterplot_compare_error
(template, specific_error)[source]
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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
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pybraincompare.compare.search.
calculate_similarity_search
(template, query_png, query_id, corr_df, button_url, image_url, max_results, absolute_value, container_width, responsive=True)[source]
calculate_similarity_search_df starts with pandas data frame to make similarity interface
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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]
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pybraincompare.compare.search.
similarity_search
(image_scores, tags, png_paths, query_png, query_id, button_url, image_url, image_ids, max_results=100, absolute_value=True, top_text=None, bottom_text=None, container_width=940, remove_scripts=None)[source]
Module contents