deid
latest
API Reference
deid.config package
Submodules
deid.config.standards module
deid.config.utils module
Module contents
deid.data package
Module contents
deid.dicom.actions package
Submodules
deid.dicom.actions.jitter module
deid.dicom.actions.uids module
Module contents
deid.dicom.pixels package
Submodules
deid.dicom.pixels.clean module
deid.dicom.pixels.detect module
Module contents
deid.dicom package
Subpackages
deid.dicom.actions package
deid.dicom.pixels package
Submodules
deid.dicom.fields module
deid.dicom.filter module
deid.dicom.groups module
deid.dicom.header module
deid.dicom.parser module
deid.dicom.tags module
deid.dicom.utils module
deid.dicom.validate module
Module contents
deid.logger package
Submodules
deid.logger.message module
deid.logger.progress module
clint.textui.progress
Module contents
deid.main package
Submodules
deid.main.identifiers module
deid.main.inspect module
Module contents
deid.utils package
Submodules
deid.utils.actions module
deid.utils.fileio module
Module contents
deid
Index
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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P
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R
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S
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T
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U
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V
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W
A
abort() (deid.logger.message.DeidMessage method)
add_field() (deid.dicom.parser.DicomParser method)
add_section() (in module deid.config.utils)
add_tag() (in module deid.dicom.tags)
addColor() (deid.logger.message.DeidMessage method)
apply_filter() (in module deid.dicom.filter)
B
bar() (in module deid.logger.progress)
basic_uuid() (in module deid.dicom.actions.uids)
blank_field() (deid.dicom.parser.DicomParser method)
C
clean() (deid.dicom.pixels.clean.DicomCleaner method)
clean_pixel_data() (in module deid.dicom.pixels.clean)
compareBase() (in module deid.dicom.filter)
contains() (in module deid.dicom.filter)
convert2boolean() (in module deid.logger.message)
create_recipe() (in module deid.tests.common)
custom() (deid.logger.message.DeidMessage method)
D
debug() (deid.logger.message.DeidMessage method)
default_font() (deid.dicom.pixels.clean.DicomCleaner method)
define() (deid.dicom.parser.DicomParser method)
deid
module
deid.config
module
deid.config.standards
module
deid.config.utils
module
deid.data
module
deid.dicom
module
deid.dicom.actions
module
deid.dicom.actions.jitter
module
deid.dicom.actions.uids
module
deid.dicom.fields
module
deid.dicom.filter
module
deid.dicom.groups
module
deid.dicom.header
module
deid.dicom.parser
module
deid.dicom.pixels
module
deid.dicom.pixels.clean
module
deid.dicom.pixels.detect
module
deid.dicom.tags
module
deid.dicom.utils
module
deid.dicom.validate
module
deid.logger
module
deid.logger.message
module
deid.logger.progress
module
deid.main
module
deid.main.identifiers
module
deid.main.inspect
module
deid.tests
module
deid.tests.common
module
deid.tests.test_clean
module
deid.tests.test_clean_pixel_dimensions
module
deid.tests.test_config
module
deid.tests.test_data
module
deid.tests.test_deid_recipe
module
deid.tests.test_dicom_fields
module
deid.tests.test_dicom_funcs
module
deid.tests.test_dicom_groups
module
deid.tests.test_dicom_tags
module
deid.tests.test_dicom_utils
module
deid.tests.test_file_meta
module
deid.tests.test_filter_detect
module
deid.tests.test_replace_identifiers
module
deid.tests.test_utils
module
deid.tests.test_utils_files
module
deid.tests.Xtest_dicom_header
module
deid.utils
module
deid.utils.actions
module
deid.utils.fileio
module
deid.version
module
DeidMessage (class in deid.logger.message)
DeidRecipe (class in deid.config)
delete_field() (deid.dicom.parser.DicomParser method)
detect() (deid.dicom.pixels.clean.DicomCleaner method)
dicom_uuid() (in module deid.dicom.actions.uids)
DicomCleaner (class in deid.dicom.pixels.clean)
DicomField (class in deid.dicom.fields)
DicomParser (class in deid.dicom.parser)
done() (deid.logger.progress.ProgressBar method)
E
emit() (deid.logger.message.DeidMessage method)
emitError() (deid.logger.message.DeidMessage method)
emitOutput() (deid.logger.message.DeidMessage method)
empty() (in module deid.dicom.filter)
endsWith() (in module deid.dicom.filter)
equals() (in module deid.dicom.filter)
equalsBase() (in module deid.dicom.filter)
error() (deid.logger.message.DeidMessage method)
evaluate_group() (in module deid.dicom.pixels.detect)
excluded_from_deletion() (deid.dicom.parser.DicomParser property)
exit() (deid.logger.message.DeidMessage method)
expand_field_expression() (in module deid.dicom.fields)
extract_coordinates() (in module deid.dicom.pixels.detect)
extract_fields_list() (in module deid.dicom.groups)
extract_item() (in module deid.dicom.fields)
extract_sequence() (in module deid.dicom.fields)
extract_values_list() (in module deid.dicom.groups)
F
find_by_name() (deid.dicom.parser.DicomParser method)
find_by_values() (deid.dicom.parser.DicomParser method)
find_deid() (in module deid.config.utils)
find_tag() (in module deid.dicom.tags)
flag() (deid.logger.message.DeidMessage method)
format_time() (deid.logger.progress.ProgressBar method)
G
get_actions() (deid.config.DeidRecipe method)
get_dataset() (in module deid.data)
get_deid() (in module deid.config.utils)
get_dicom() (in module deid.tests.common)
(in module deid.tests.Xtest_dicom_header)
get_fields() (deid.dicom.parser.DicomParser method)
(in module deid.dicom.fields)
get_fields_lists() (deid.config.DeidRecipe method)
get_figure() (deid.dicom.pixels.clean.DicomCleaner method)
get_file() (in module deid.tests.common)
(in module deid.tests.test_clean_pixel_dimensions)
get_files() (in module deid.dicom.utils)
get_filters() (deid.config.DeidRecipe method)
get_format() (deid.config.DeidRecipe method)
get_func() (in module deid.utils.actions)
get_identifiers() (in module deid.dicom.header)
get_installdir() (in module deid.utils.fileio)
get_logging_level() (in module deid.logger.message)
get_logs() (deid.logger.message.DeidMessage method)
get_nested_field() (deid.dicom.parser.DicomParser method)
get_parser() (in module deid.main)
get_private() (in module deid.dicom.tags)
get_same_file() (in module deid.tests.common)
get_tag() (in module deid.dicom.tags)
get_temporary_name() (in module deid.utils.fileio)
get_timestamp() (in module deid.utils.actions)
get_user_color_preference() (in module deid.logger.message)
get_values_lists() (deid.config.DeidRecipe method)
H
has_actions() (deid.config.DeidRecipe method)
has_burned_pixels() (in module deid.dicom.pixels.detect)
has_fields_lists() (deid.config.DeidRecipe method)
has_private() (in module deid.dicom.tags)
has_values_lists() (deid.config.DeidRecipe method)
I
info() (deid.logger.message.DeidMessage method)
is_number() (in module deid.utils.fileio)
is_quiet() (deid.logger.message.DeidMessage method)
isEnabledFor() (deid.logger.message.DeidMessage method)
J
jitter_timestamp() (in module deid.dicom.actions.jitter)
jitter_timestamp_func() (in module deid.dicom.actions.jitter)
K
keep() (deid.dicom.parser.DicomParser property)
L
listof() (deid.config.DeidRecipe method)
load() (deid.config.DeidRecipe method)
(deid.dicom.parser.DicomParser method)
load_combined_deid() (in module deid.config.utils)
load_deid() (in module deid.config.utils)
load_dicom() (in module deid.dicom.utils)
log() (deid.logger.message.DeidMessage method)
ls_fieldlists() (deid.config.DeidRecipe method)
ls_filters() (deid.config.DeidRecipe method)
ls_valuelists() (deid.config.DeidRecipe method)
M
main() (in module deid.main)
(in module deid.main.identifiers)
(in module deid.main.inspect)
matches() (in module deid.dicom.filter)
missing() (in module deid.dicom.filter)
module
deid
deid.config
deid.config.standards
deid.config.utils
deid.data
deid.dicom
deid.dicom.actions
deid.dicom.actions.jitter
deid.dicom.actions.uids
deid.dicom.fields
deid.dicom.filter
deid.dicom.groups
deid.dicom.header
deid.dicom.parser
deid.dicom.pixels
deid.dicom.pixels.clean
deid.dicom.pixels.detect
deid.dicom.tags
deid.dicom.utils
deid.dicom.validate
deid.logger
deid.logger.message
deid.logger.progress
deid.main
deid.main.identifiers
deid.main.inspect
deid.tests
deid.tests.common
deid.tests.test_clean
deid.tests.test_clean_pixel_dimensions
deid.tests.test_config
deid.tests.test_data
deid.tests.test_deid_recipe
deid.tests.test_dicom_fields
deid.tests.test_dicom_funcs
deid.tests.test_dicom_groups
deid.tests.test_dicom_tags
deid.tests.test_dicom_utils
deid.tests.test_file_meta
deid.tests.test_filter_detect
deid.tests.test_replace_identifiers
deid.tests.test_utils
deid.tests.test_utils_files
deid.tests.Xtest_dicom_header
deid.utils
deid.utils.actions
deid.utils.fileio
deid.version
N
name_contains() (deid.dicom.fields.DicomField method)
newline() (deid.logger.message.DeidMessage method)
notContains() (in module deid.dicom.filter)
notEquals() (in module deid.dicom.filter)
P
parse() (deid.dicom.parser.DicomParser method)
parse_config_action() (in module deid.config.utils)
parse_filter_group() (in module deid.config.utils)
parse_format() (in module deid.config.utils)
parse_group_action() (in module deid.config.utils)
parse_keyvalue_pairs() (in module deid.utils.actions)
parse_label() (in module deid.config.utils)
parse_member() (in module deid.config.utils)
parse_value() (in module deid.utils.actions)
perform_action() (deid.dicom.parser.DicomParser method)
ProgressBar (class in deid.logger.progress)
pydicom_uuid() (in module deid.dicom.actions.uids)
R
read_file() (in module deid.utils.fileio)
read_json() (in module deid.utils.fileio)
recursive_find() (in module deid.utils.fileio)
remove_private() (deid.dicom.parser.DicomParser method)
remove_private_identifiers() (in module deid.dicom.header)
remove_sequences() (in module deid.dicom.tags)
replace_field() (deid.dicom.parser.DicomParser method)
replace_identifiers() (in module deid.dicom.header)
reset_preamble() (deid.dicom.parser.DicomParser method)
S
save() (deid.dicom.parser.DicomParser method)
save_animation() (deid.dicom.pixels.clean.DicomCleaner method)
save_dicom() (deid.dicom.pixels.clean.DicomCleaner method)
(in module deid.dicom.utils)
save_png() (deid.dicom.pixels.clean.DicomCleaner method)
select_matches() (deid.dicom.fields.DicomField method)
setUp() (deid.tests.test_clean.TestClean method)
(deid.tests.test_clean_pixel_dimensions.TestCleanPizelDimensions method)
(deid.tests.test_config.TestConfig method)
(deid.tests.test_data.TestUtils method)
(deid.tests.test_deid_recipe.TestDeidRecipe method)
(deid.tests.test_dicom_fields.TestDicomFields method)
(deid.tests.test_dicom_funcs.TestDicomFuncs method)
(deid.tests.test_dicom_groups.TestDicomGroups method)
(deid.tests.test_dicom_tags.TestDicomTags method)
(deid.tests.test_dicom_utils.TestDicomUtils method)
(deid.tests.test_file_meta.TestDicom method)
(deid.tests.test_filter_detect.TestFilterDetect method)
(deid.tests.test_replace_identifiers.TestDicom method)
(deid.tests.test_utils.TestUtils method)
(deid.tests.test_utils_files.TestDicom method)
(deid.tests.Xtest_dicom_header.TestDicomHeader method)
show() (deid.logger.progress.ProgressBar method)
show_progress() (deid.logger.message.DeidMessage method)
skip() (deid.dicom.parser.DicomParser property)
startsWith() (in module deid.dicom.filter)
stripped_tag() (deid.dicom.fields.DicomField property)
suffix_uuid() (in module deid.dicom.actions.uids)
T
table() (deid.logger.message.DeidMessage method)
tag() (deid.dicom.fields.DicomField property)
tearDown() (deid.tests.test_clean.TestClean method)
(deid.tests.test_clean_pixel_dimensions.TestCleanPizelDimensions method)
(deid.tests.test_config.TestConfig method)
(deid.tests.test_data.TestUtils method)
(deid.tests.test_deid_recipe.TestDeidRecipe method)
(deid.tests.test_dicom_fields.TestDicomFields method)
(deid.tests.test_dicom_funcs.TestDicomFuncs method)
(deid.tests.test_dicom_groups.TestDicomGroups method)
(deid.tests.test_dicom_tags.TestDicomTags method)
(deid.tests.test_dicom_utils.TestDicomUtils method)
(deid.tests.test_filter_detect.TestFilterDetect method)
(deid.tests.test_replace_identifiers.TestDicom method)
(deid.tests.test_utils.TestUtils method)
(deid.tests.test_utils_files.TestDicom method)
(deid.tests.Xtest_dicom_header.TestDicomHeader method)
test_2d_Greyscale_image() (deid.tests.test_clean_pixel_dimensions.TestCleanPizelDimensions method)
test_2d_Greyscale_image_all() (deid.tests.test_clean_pixel_dimensions.TestCleanPizelDimensions method)
test_3d_Greyscale_cine_clip() (deid.tests.test_clean_pixel_dimensions.TestCleanPizelDimensions method)
test_3d_Greyscale_cine_clip_all() (deid.tests.test_clean_pixel_dimensions.TestCleanPizelDimensions method)
test_3d_RGB_image() (deid.tests.test_clean_pixel_dimensions.TestCleanPizelDimensions method)
test_3d_RGB_image_all() (deid.tests.test_clean_pixel_dimensions.TestCleanPizelDimensions method)
test_4d_RGB_cine_clip() (deid.tests.test_clean_pixel_dimensions.TestCleanPizelDimensions method)
test_4d_RGB_cine_clip_all() (deid.tests.test_clean_pixel_dimensions.TestCleanPizelDimensions method)
test_add_private_constant() (deid.tests.test_replace_identifiers.TestDicom method)
test_add_private_constant_save_true() (deid.tests.test_replace_identifiers.TestDicom method)
test_add_public_constant() (deid.tests.test_replace_identifiers.TestDicom method)
test_add_tag_variable() (deid.tests.test_replace_identifiers.TestDicom method)
test_add_tag_variable_save_true() (deid.tests.test_replace_identifiers.TestDicom method)
test_addremove_compounding() (deid.tests.test_replace_identifiers.TestDicom method)
test_basic_uuid() (deid.tests.test_dicom_funcs.TestDicomFuncs method)
test_blank_field_keep_field_compounding_should_keep() (deid.tests.test_replace_identifiers.TestDicom method)
test_dicom_jitter() (deid.tests.test_dicom_funcs.TestDicomFuncs method)
test_dicom_uuid() (deid.tests.test_dicom_funcs.TestDicomFuncs method)
test_expander_except() (deid.tests.test_replace_identifiers.TestDicom method)
test_expanders() (deid.tests.test_replace_identifiers.TestDicom method)
test_extract_groups() (deid.tests.test_dicom_groups.TestDicomGroups method)
test_field_expansion() (deid.tests.test_dicom_fields.TestDicomFields method)
test_fieldset_remove() (deid.tests.test_replace_identifiers.TestDicom method)
test_fieldset_remove_private() (deid.tests.test_replace_identifiers.TestDicom method)
test_filter_multiple_first_filter_match() (deid.tests.test_filter_detect.TestFilterDetect method)
test_filter_multiple_rule_innerop_false() (deid.tests.test_filter_detect.TestFilterDetect method)
test_filter_multiple_second_filter_match() (deid.tests.test_filter_detect.TestFilterDetect method)
test_filter_multiple_two_filter_match() (deid.tests.test_filter_detect.TestFilterDetect method)
test_filter_multiple_zero_filter_match() (deid.tests.test_filter_detect.TestFilterDetect method)
test_filter_multple_rule_innerop_true() (deid.tests.test_filter_detect.TestFilterDetect method)
test_filter_single_rule_false() (deid.tests.test_filter_detect.TestFilterDetect method)
test_filter_single_rule_innerop_false() (deid.tests.test_filter_detect.TestFilterDetect method)
test_filter_single_rule_innerop_true() (deid.tests.test_filter_detect.TestFilterDetect method)
test_filter_single_rule_true() (deid.tests.test_filter_detect.TestFilterDetect method)
test_find_deid() (deid.tests.test_config.TestConfig method)
test_get_dataset() (deid.tests.test_data.TestUtils method)
test_get_fields() (deid.tests.Xtest_dicom_header.TestDicomHeader method)
test_get_files() (deid.tests.test_dicom_utils.TestDicomUtils method)
(deid.tests.test_utils_files.TestDicom method)
test_get_files_as_list() (deid.tests.test_dicom_utils.TestDicomUtils method)
(deid.tests.test_utils_files.TestDicom method)
test_get_functions() (deid.tests.test_deid_recipe.TestDeidRecipe method)
test_get_identifiers() (deid.tests.Xtest_dicom_header.TestDicomHeader method)
test_get_installdir() (deid.tests.test_utils.TestUtils method)
test_get_tag() (deid.tests.test_dicom_tags.TestDicomTags method)
test_get_temporary_name() (deid.tests.test_utils.TestUtils method)
test_jitter_blank_date() (deid.tests.test_replace_identifiers.TestDicom method)
test_jitter_compounding() (deid.tests.test_replace_identifiers.TestDicom method)
test_jitter_date() (deid.tests.test_replace_identifiers.TestDicom method)
test_jitter_private_tag() (deid.tests.test_replace_identifiers.TestDicom method)
test_jitter_replace_compounding() (deid.tests.test_replace_identifiers.TestDicom method)
test_jitter_timestamp() (deid.tests.test_dicom_utils.TestDicomUtils method)
(deid.tests.test_replace_identifiers.TestDicom method)
test_jitter_values() (deid.tests.test_replace_identifiers.TestDicom method)
test_load_deid() (deid.tests.test_config.TestConfig method)
test_load_recipe() (deid.tests.test_deid_recipe.TestDeidRecipe method)
test_nested_replace() (deid.tests.test_replace_identifiers.TestDicom method)
test_pixel_cleaner_keepcoordinates() (deid.tests.test_clean.TestClean method)
test_pixel_cleaner_keepcoordinates_from() (deid.tests.test_clean.TestClean method)
test_pixel_cleaner_keepcoordinates_noaction() (deid.tests.test_clean.TestClean method)
test_pixel_cleaner_remove_all() (deid.tests.test_clean.TestClean method)
test_pixel_cleaner_remove_coordinates() (deid.tests.test_clean.TestClean method)
test_pixel_cleaner_remove_coordinates_dicom_file() (deid.tests.test_clean.TestClean method)
test_pixel_cleaner_remove_multiple() (deid.tests.test_clean.TestClean method)
test_pixel_cleaner_remove_multiple_filters() (deid.tests.test_clean.TestClean method)
test_pydicom_uuid() (deid.tests.test_dicom_funcs.TestDicomFuncs method)
test_recursive_find() (deid.tests.test_utils.TestUtils method)
test_remove() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_all_add_field_compounding_should_add() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_all_blank_field_compounding_should_remove() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_all_func() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_all_jitter_one_should_jitter() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_all_keep_field_compounding_should_keep() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_all_keep_one_jitter_it_should_keep() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_all_keep_one_replace_it_should_keep() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_all_replace_one_should_replace() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_except_field_keep_other_field_compounding_should_keep() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_except_is_acting_as_substring() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_field_jitter_it_should_jitter() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_field_keep_same_field_compounding_should_keep() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_field_replace_it_should_replace() (deid.tests.test_replace_identifiers.TestDicom method)
test_remove_keep_add_field_compounding_should_add() (deid.tests.test_replace_identifiers.TestDicom method)
test_removeadd_compounding() (deid.tests.test_replace_identifiers.TestDicom method)
test_replace_filemeta() (deid.tests.test_file_meta.TestDicom method)
test_replace_identifiers() (deid.tests.Xtest_dicom_header.TestDicomHeader method)
test_replace_protected_field() (deid.tests.test_file_meta.TestDicom method)
test_replace_with_constant() (deid.tests.test_replace_identifiers.TestDicom method)
test_standards() (deid.tests.test_config.TestConfig method)
test_strip_sequences() (deid.tests.test_replace_identifiers.TestDicom method)
test_suffix_uuid() (deid.tests.test_dicom_funcs.TestDicomFuncs method)
test_tag_expanders_midtag() (deid.tests.test_replace_identifiers.TestDicom method)
test_tag_expanders_tagelement() (deid.tests.test_replace_identifiers.TestDicom method)
test_tag_expanders_taggroup() (deid.tests.test_replace_identifiers.TestDicom method)
test_user_provided_func() (deid.tests.test_dicom_funcs.TestDicomFuncs method)
test_valueset_empty_remove() (deid.tests.test_replace_identifiers.TestDicom method)
test_valueset_private() (deid.tests.test_replace_identifiers.TestDicom method)
test_valueset_remove() (deid.tests.test_replace_identifiers.TestDicom method)
test_valueset_remove_one_empty() (deid.tests.test_replace_identifiers.TestDicom method)
test_write_read_files() (deid.tests.test_utils.TestUtils method)
TestClean (class in deid.tests.test_clean)
TestCleanPizelDimensions (class in deid.tests.test_clean_pixel_dimensions)
TestConfig (class in deid.tests.test_config)
TestDeidRecipe (class in deid.tests.test_deid_recipe)
TestDicom (class in deid.tests.test_file_meta)
(class in deid.tests.test_replace_identifiers)
(class in deid.tests.test_utils_files)
TestDicomFields (class in deid.tests.test_dicom_fields)
TestDicomFuncs (class in deid.tests.test_dicom_funcs)
TestDicomGroups (class in deid.tests.test_dicom_groups)
TestDicomHeader (class in deid.tests.Xtest_dicom_header)
TestDicomTags (class in deid.tests.test_dicom_tags)
TestDicomUtils (class in deid.tests.test_dicom_utils)
TestFilterDetect (class in deid.tests.test_filter_detect)
TestUtils (class in deid.tests.test_data)
(class in deid.tests.test_utils)
to_int() (in module deid.utils.fileio)
U
update_tag() (in module deid.dicom.tags)
useColor() (deid.logger.message.DeidMessage method)
V
validate_dicoms() (in module deid.dicom.validate)
value_contains() (deid.dicom.fields.DicomField method)
verbose() (deid.logger.message.DeidMessage method)
verbose1() (deid.logger.message.DeidMessage method)
verbose2() (deid.logger.message.DeidMessage method)
verbose3() (deid.logger.message.DeidMessage method)
W
warning() (deid.logger.message.DeidMessage method)
write() (deid.logger.message.DeidMessage method)
write_file() (in module deid.utils.fileio)
write_json() (in module deid.utils.fileio)
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