def define_ciod_module_relationship(ciod, module):
try:
usage, conditional_statement = expand_conditional_statement(
module['usage'])
except KeyError as e:
# TODO: Remove try/except block once missing IE column in Table A.85.1-1 is fixed (Related to Issue #17)
if 'Common Instance Reference' in module['informationEntity']:
# Shift every column right by one and replace missing IE column
module['usage'] = module['reference_fragment']
module['reference_fragment'] = module['module']
module['module'] = module['informationEntity']
module[
'informationEntity'] = "<td align=\"left\" colspan=\"1\" rowspan=\"1\">\n<p>\n<a id=\"para_040bd3bd-9a9f-4066-8431-ea1ded2a909e\" shape=\"rect\"></a>Encapsulated Document</p>\n</td>"
usage, conditional_statement = expand_conditional_statement(
module['usage'])
else:
raise e
informationEntity = pl.text_from_html_string(module['informationEntity'])
# TODO: Remove if block once missing IE column in Table A.32.10-1 is fixed (Issue #17)
if (not informationEntity and ciod == 'Real-Time Video Photographic Image'
and any(
mod in module['module'] for mod in
['Real-Time Acquisition', 'Current Frame Functional Groups'])):
# Manually input missing field
informationEntity = 'Image'
return {
"ciodId": pl.create_slug(ciod),
"moduleId": pl.create_slug(pl.text_from_html_string(module['module'])),
"usage": usage,
"conditionalStatement": conditional_statement,
"informationEntity": informationEntity
}
def define_ciod_macro_relationship(ciod, macro):
usage, conditional_statement = expand_conditional_statement(macro['usage'])
return {
"ciodId": pl.create_slug(ciod),
"macroId": pl.create_slug(clean_macro_name(pl.text_from_html_string(macro['macro']))),
"usage": usage,
"conditionalStatement": conditional_statement
}
def define_ciod_module_relationship(ciod, module):
usage, conditional_statement = expand_conditional_statement(
module['usage'])
return {
"ciod": pl.create_slug(ciod),
"module": pl.create_slug(pl.text_from_html_string(module['module'])),
"usage": usage,
"conditionalStatement": conditional_statement,
"informationEntity":
pl.text_from_html_string(module['informationEntity'])
}
def table_to_json(table: List[TableDictType]) -> List[TableDictType]:
attributes = []
for attr in table:
attr['id'] = pl.create_slug(attr['tag'])
attr['tag'] = attr['tag'].upper()
attributes.append(attr)
return attributes
def update_hierarchy_position(attr: Dict[str, str], last_id: List[str],
current_level: int) -> Tuple[List[str], int]:
attr_id = pl.create_slug(clean_attribute_field(attr['tag']))
attribute_level = get_hierarchy_level(attr['name'])
delta_l = attribute_level - current_level
if attr_id == 'none':
print(attr)
raise Exception('this shouldn\'t happen')
if delta_l > 1:
# Standard workaround: There is a typo in the DICOM standard where two hierarchy
# markers are used instead of one. This catches that anomaly.
delta_l = 1
# Error can be seen at the following link:
# http://dicom.nema.org/medical/dicom/current/output/html/part03.html#para_a3f9cf09-67b7-4645-943a-6d405dc81b93
# raise Exception('Shouldn\'t be skipping levels.')
if delta_l == 0:
last_id[-1] = attr_id
elif delta_l == 1:
last_id.append(attr_id)
current_level += 1
elif delta_l < 0:
last_id = last_id[:(delta_l)]
last_id[-1] = attr_id
current_level += (delta_l)
return last_id, current_level
def get_table_with_metadata(
table_with_tdiv: Tuple[List[TableDictType], Tag]) -> MetadataTableType:
table, tdiv = table_with_tdiv
table_name = pr.table_name(tdiv)
clean_name = pl.clean_table_name(table_name)
table_description = pr.table_description(tdiv)
is_macro = True if MACRO_TABLE_SUFFIX.match(table_name) else False
# Standard workaround: Add description to module without a description paragraph
# http://dicom.nema.org/dicom/2013/output/chtml/part03/sect_F.3.html#sect_F.3.2.1
if table_description.has_attr(
'class') and 'title' in table_description.get('class'):
table_description_str = f'<p>{clean_name} {"Macro" if is_macro else "Module"}.</p>'
table_description = BeautifulSoup(table_description_str, 'html.parser')
return {
'name':
clean_name,
'attributes':
table,
'id':
pl.create_slug(clean_name),
'description':
str(clean_table_description(table_description, is_macro)),
'linkToStandard':
fix_nonstandard_section_links(get_short_standard_link(tdiv)),
'isMacro':
is_macro,
}
def define_ciod_module_relationship(ciod, module):
try:
usage, conditional_statement = expand_conditional_statement(
module['usage'])
except KeyError as e:
# TODO: Remove try/except block once missing IE column in Table A.85.1-1 is fixed (Related to Issue #17)
if 'Common Instance Reference' in module['informationEntity']:
# Shift every column right by one and replace missing IE column
module['usage'] = module['referenceFragment']
module['referenceFragment'] = module['module']
module['module'] = module['informationEntity']
module[
'informationEntity'] = "<td align=\"left\" colspan=\"1\" rowspan=\"1\">\n<p>\n<a id=\"para_040bd3bd-9a9f-4066-8431-ea1ded2a909e\" shape=\"rect\"></a>Encapsulated Document</p>\n</td>"
usage, conditional_statement = expand_conditional_statement(
module['usage'])
else:
raise e
raw_information_entity = module.get('informationEntity')
# If the "Information Entity" field doesn't exist, this is probably an single IOD rather than a CIOD, so just use the IOD name
information_entity = pl.text_from_html_string(
raw_information_entity) if raw_information_entity else ciod
# Standard workaround: Fill in missing values in the "Information Entity" field of certain rows in Table A.32.10-1
# http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.32.10.2.html#table_A.32.10-1
if (ciod == 'Real-Time Video Photographic Image' and
any(mod in module['module'] for mod in
['Real-Time Acquisition', 'Current Frame Functional Groups'])):
# Manually input missing field
information_entity = 'Image'
ciod_id = pl.create_slug(ciod)
module_id = pl.create_slug(pl.text_from_html_string(module['module']))
# Standard workaround: Fix inconsistent capitalization in the "Information Entity" field of Rendition Selection Document
# http://dicom.nema.org/medical/dicom/2019e/output/chtml/part03/sect_A.35.21.3.html#table_A.35.21-1
if ciod == 'Rendition Selection Document' and module_id == 'synchronization':
information_entity = 'Frame of Reference'
# Create CIOD-specific "Multi-frame Functional Group" module IDs
if module_id == MF_FUNC_GROUP_MODULE_ID:
module_id = f'{ciod_id}-{module_id}'
# Create CIOD-specific "Current Frame Functional Group" module IDs
if module_id == CF_FUNC_GROUP_MODULE_ID:
module_id = f'{ciod_id}-{module_id}'
return {
"ciodId": ciod_id,
"moduleId": module_id,
"usage": usage,
"conditionalStatement": conditional_statement,
"informationEntity": information_entity,
}
def attribute_table_to_json(table: List[TableDictType]) -> List[TableDictType]:
attributes = []
for attr in table:
attr['id'] = pl.create_slug(attr['tag'])
attr['tag'] = attr['tag'].upper()
attr['retired'] = 'Y' if 'RET' in attr['retired'] else 'N'
attributes.append(attr)
return attributes
def attribute_table_to_json(table):
attribute_dict = {}
for attr in table:
attr_slug = pl.create_slug(attr['tag'])
attribute_dict[attr_slug] = attr
attribute_dict[attr_slug]['tag'] = attr['tag'].upper()
attribute_dict[attr_slug][
'retired'] = True if attr['retired'] == 'RET' else False
return attribute_dict
def get_table_with_metadata(table_with_tdiv):
table, tdiv = table_with_tdiv
clean_name = pl.clean_table_name(pr.table_name(tdiv))
table_description = get_ciod_description(tdiv)
return {
'name': clean_name,
'modules': table,
'id': pl.create_slug(clean_name),
'description': str(table_description),
'linkToStandard': get_short_standard_link(tdiv)
}
def get_table_with_metadata(
table_with_tdiv: Tuple[List[TableDictType], Tag]) -> MetadataTableType:
table, tdiv = table_with_tdiv
clean_name = clean_macro_table_name(pr.table_name(tdiv))
table_description = get_table_description(tdiv)
return {
'name': clean_name,
'macros': table,
'id': pl.create_slug(clean_name),
'description': str(table_description),
'linkToStandard': get_short_standard_link(tdiv)
}
def get_table_with_metadata(table_with_tdiv: Tuple[List[TableDictType], Tag]) -> MetadataTableType:
table, tdiv = table_with_tdiv
clean_name = clean_macro_table_name(pr.table_name(tdiv))
clean_description = pl.clean_html(str(tdiv.find_previous('p')))
module_type = 'Multi-frame' if 'Multi-frame' in clean_description \
else 'Current Frame' if 'Current Frame' in clean_description \
else None
return {
'name': clean_name,
'macros': table,
'id': pl.create_slug(clean_name),
'description': clean_description,
'linkToStandard': get_short_standard_link(tdiv),
'moduleType': module_type,
}
def update_hierarchy_position(attr: Dict[str, str], last_id: List[str],
current_level: int) -> Tuple[List[str], int]:
attr_id = pl.create_slug(clean_attribute_field(attr['tag']))
attribute_level = get_hierarchy_level(attr['name'])
delta_l = attribute_level - current_level
if attr_id == 'none':
print(attr)
raise Exception('this shouldn\'t happen')
if delta_l > 1:
# Standard workaround: Catch typo in Table C.8.25.16-8 where an include
# statement uses two hierarchy markers instead of one
# http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.8.25.16.8.html
delta_l = 1
if delta_l == 0:
last_id[-1] = attr_id
elif delta_l == 1:
last_id.append(attr_id)
current_level += 1
elif delta_l < 0:
last_id = last_id[:(delta_l)]
last_id[-1] = attr_id
current_level += (delta_l)
return last_id, current_level