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Account for added column in IOD and UID tables
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- UID Table in PS3.6 got additional Keyword column
- IOD Table in PS3.4 got additional Specialization column
- fixes #3
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@mrbean-bremen
mrbean-bremen committed Jan 24, 2021
1 parent 25b23ef commit 5b1ac6a
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Showing 11 changed files with 247 additions and 137 deletions.
2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ it if found.

It is also possible to use older versions of the standard via a command line
option, provided they are still available for download (at the time of
writing, standards are available from 2014a to 2018b).
writing, standards are available since 2014a).

dcm_dump_info
-------------
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1 change: 0 additions & 1 deletion dcm_spec_tools/spec_reader/condition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,4 +131,3 @@ def to_string(self, dict_info):
elif self.operator == '>':
result += ' is greater than ' + self.values[0]
return result

18 changes: 12 additions & 6 deletions dcm_spec_tools/spec_reader/condition_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,8 @@ def _tag_id(tag_id_string):
def _parse_tag(self, tag_string):
match = self.tag_expression.match(tag_string.strip())
if match:
value_index = 0 if match.group('index') is None else int(match.group('index')) - 1
value_index = (0 if match.group('index') is None
else int(match.group('index')) - 1)
if match.group('id') is not None:
return match.group('id'), value_index
tag_name = match.group('name').strip()
Expand Down Expand Up @@ -177,8 +178,10 @@ def extract_value_string(self, value_string):
continue
if end_index > 0:
if value_string.find(' or ') in [end_index, end_index + 1]:
# differentiate between several values and several conditions - check if the rest is a condition
or_cond = self._parse_tag_expressions(value_string[end_index + 3:])
# differentiate between several values and several
# conditions - check if the rest is a condition
or_cond = self._parse_tag_expressions(
value_string[end_index + 3:])
if or_cond.type == 'U':
start_index = end_index + 4
continue
Expand All @@ -199,7 +202,8 @@ def _parse_tag_expressions(self, condition, nested=False):
condition = rest[len(operator) + 1:]
break
if logical_op is not None:
next_result = self._parse_tag_expressions(condition, nested=True)
next_result = self._parse_tag_expressions(
condition, nested=True)
if next_result.type != 'U':
next_result.type = None
new_result = Condition(ctype=result.type)
Expand Down Expand Up @@ -250,13 +254,15 @@ def _parse_multiple_tags(self, condition, operator, values, logical_op):
result = Condition()
cond_list = self._condition_list(logical_op, result)
for tag_string in condition.split(', '):
tag_result = self._result_from_tag_string(tag_string, operator, values)
tag_result = self._result_from_tag_string(
tag_string, operator, values)
if tag_result:
cond_list.append(tag_result)
if len(cond_list) > 1:
return result

def _condition_list(self, logical_op, result):
@staticmethod
def _condition_list(logical_op, result):
cond_list = (result.and_conditions if logical_op == 'and'
else result.or_conditions)
return cond_list
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16 changes: 6 additions & 10 deletions dcm_spec_tools/spec_reader/edition_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,25 +4,20 @@
import os
import re
import sys
from abc import ABC

from dcm_spec_tools import __version__
from dcm_spec_tools.spec_reader.part3_reader import Part3Reader
from dcm_spec_tools.spec_reader.part4_reader import Part4Reader
from dcm_spec_tools.spec_reader.part6_reader import Part6Reader
from dcm_spec_tools.spec_reader.serializer import DefinitionEncoder

try:
from urllib import urlretrieve
except ImportError:
from urllib.request import urlretrieve
from urllib.request import urlretrieve

try:
import HTMLParser as html_parser
except ImportError:
import html.parser as html_parser
import html.parser as html_parser


class EditionParser(html_parser.HTMLParser):
class EditionParser(html_parser.HTMLParser, ABC):
edition_re = re.compile(r'\d\d\d\d[a-h]')

def __init__(self):
Expand Down Expand Up @@ -125,7 +120,8 @@ def get_edition(self, revision):

def is_current(self, revision):
"""Get the edition matching the revision or None.
The revision can be the edition name, the year of the edition, or 'current'.
The revision can be the edition name, the year of the edition,
or 'current'.
"""
if revision is None:
return True
Expand Down
108 changes: 70 additions & 38 deletions dcm_spec_tools/spec_reader/part3_reader.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
"""
Chapter3Reader collects DICOM Information Object Definition information for specific Storage SOP Classes.
Chapter3Reader collects DICOM Information Object Definition information
for specific Storage SOP Classes.
The information is taken from PS3.3 in docbook format as provided by ACR NEMA.
"""
import logging
Expand All @@ -8,7 +9,9 @@
import sys

from dcm_spec_tools.spec_reader.condition_parser import ConditionParser
from dcm_spec_tools.spec_reader.spec_reader import SpecReader, SpecReaderParseError, SpecReaderLookupError
from dcm_spec_tools.spec_reader.spec_reader import (
SpecReader, SpecReaderParseError, SpecReaderLookupError
)


class Part3Reader(SpecReader):
Expand All @@ -33,11 +36,13 @@ def iod_description(self, chapter):
"""Return the IOD information for the given chapter.
The return value is a dict with the entries:
'title': The display name of the IOD
'modules': A dictionary of the contained IOD modules with the module name as key.
A module dict value has the following entries:
'ref': The section in PS3.3 describing the module (e.g. 'C.7.4.2')
'use': Usage information (e.g. 'M' for mandatory)
'title': The display name of the IOD
'modules': A dictionary of the contained IOD modules with the
module name as key.
A module dict value has the following entries:
'ref': The section in PS3.3 describing the module
(e.g. 'C.7.4.2')
'use': Usage information (e.g. 'M' for mandatory)
Raises SpecReaderLookupError if the chapter is not found.
"""
if chapter not in self._iod_descriptions:
Expand All @@ -48,29 +53,33 @@ def iod_description(self, chapter):
try:
return self._iod_descriptions[chapter]
except KeyError:
raise SpecReaderLookupError('No definition found for chapter {}'.format(chapter))
raise SpecReaderLookupError(
'No definition found for chapter {}'.format(chapter))

def iod_descriptions(self):
"""Return the IOD information dict per chapter.
The dict has the chapter (e.g. 'A.3') as key and the IOD descriptions as value.
The dict has the chapter (e.g. 'A.3') as key and the IOD descriptions
as value.
See iod_description() for the format of the IOD descriptions.
Retired IODs (which have no module list) are omitted.
"""
return {chapter: self.iod_description(chapter) for chapter in self._get_iod_nodes()
return {chapter: self.iod_description(chapter) for chapter in
self._get_iod_nodes()
if self.iod_description(chapter)['modules']}

def module_description(self, section):
"""Return the module information in the given section.
The return value is a dict with the entries:
'title': The name of the module
'attributes': A dictionary of the contained module attributes with the tag as key.
An attribute dict value has the following entries:
'name': the tag name
'type': the type (1, 1C, 2, 2C, 3)
'items': only for sequence tags - contains a dictionary
of the module attributes contained in the sequence
'title': The name of the module
'attributes': A dictionary of the contained module attributes
with the tag as key.
An attribute dict value has the following entries:
'name': the tag name
'type': the type (1, 1C, 2, 2C, 3)
'items': only for sequence tags - contains a dictionary
of the module attributes contained in the sequence
Raises SpecReaderLookupError if the section is not found.
"""
if section not in self._module_descriptions:
Expand All @@ -81,12 +90,14 @@ def module_description(self, section):
try:
return self._module_descriptions[section]
except KeyError:
raise SpecReaderLookupError('No definition found for section {}'.format(section))
raise SpecReaderLookupError(
'No definition found for section {}'.format(section))

def module_descriptions(self):
"""Return the module attribute information for all IODs.
The return value is a dict with the section name as key and a description dict as value.
The return value is a dict with the section name as key and
a description dict as value.
See module_description() for the content of the value dict.
"""
# ensure that all module attributes are read
Expand All @@ -95,7 +106,8 @@ def module_descriptions(self):

def _get_iod_nodes(self):
if not self._iod_nodes:
chapter_a = self._find(self._get_doc_root(), ['chapter[@label="A"]'])
chapter_a = self._find(self._get_doc_root(),
['chapter[@label="A"]'])
if chapter_a is None:
raise SpecReaderParseError('Chapter A in Part 3 not found')
# ignore A.1
Expand All @@ -109,13 +121,16 @@ def _get_iod_nodes(self):
iod_sub_nodes = []
nodes_with_subnodes = []
for iod_node in all_iod_nodes:
sub_nodes = self._find_sections_with_title_endings(iod_node, iod_def_endings)
sub_nodes = self._find_sections_with_title_endings(
iod_node, iod_def_endings)
if sub_nodes:
nodes_with_subnodes.append(iod_node)
iod_sub_nodes.extend(sub_nodes)
all_iod_nodes = [node for node in all_iod_nodes if node not in nodes_with_subnodes]
all_iod_nodes = [node for node in all_iod_nodes if
node not in nodes_with_subnodes]
all_iod_nodes.extend(iod_sub_nodes)
self._iod_nodes = {node.attrib['label']: node for node in all_iod_nodes}
self._iod_nodes = {node.attrib['label']: node for node in
all_iod_nodes}
return self._iod_nodes

def _get_section_node(self, section):
Expand Down Expand Up @@ -171,14 +186,16 @@ def _handle_included_attributes(self, columns, current_descriptions):
if label not in self._module_descriptions:
ref_node = self._get_ref_node(element, label)
if ref_node is None:
raise SpecReaderLookupError('Failed to lookup include reference ' + include_ref)
raise SpecReaderLookupError(
'Failed to lookup include reference ' + include_ref)
# it is allowed to have no attributes (example: Raw Data)
ref_description = self._parse_module_description(ref_node) or {}
self._module_descriptions[label] = ref_description
current_descriptions[-1].setdefault('include', []).append(label)
self._current_refs.pop()

def _handle_regular_attribute(self, columns, current_descriptions, last_tag_id, tag_name):
def _handle_regular_attribute(self, columns, current_descriptions,
last_tag_id, tag_name):
tag_id = self._find_text(columns[1])
tag_type = self._find_text(columns[2])
if tag_id:
Expand All @@ -191,14 +208,16 @@ def _handle_regular_attribute(self, columns, current_descriptions, last_tag_id,
# index = cond.find('Required if ')
# if index >= 0:
# current_descriptions[-1][tag_id]['desc'] = cond[index:]
current_descriptions[-1][tag_id]['cond'] = self._condition_parser.parse(
current_descriptions[-1][tag_id][
'cond'] = self._condition_parser.parse(
self._find_all_text(columns[3]))

last_tag_id = tag_id
return last_tag_id

def _get_ref_node(self, element, label):
return self._get_doc_tree().find('.//{}{}[@label="{}"]'.format(self.docbook_ns, element, label))
return self._get_doc_tree().find(
'.//{}{}[@label="{}"]'.format(self.docbook_ns, element, label))

@staticmethod
def _get_ref_element_and_label(ref):
Expand All @@ -207,7 +226,8 @@ def _get_ref_element_and_label(ref):
element = 'section'
return element, label

def _get_tag_name_and_level(self, column, current_descriptions, current_level, last_tag_id):
def _get_tag_name_and_level(self, column, current_descriptions,
current_level, last_tag_id):
tag_name = self._find_text(column)
if not tag_name:
return '', 0
Expand All @@ -217,7 +237,8 @@ def _get_tag_name_and_level(self, column, current_descriptions, current_level, l
if level > current_level:
sequence_description = {}
try:
current_descriptions[-1][last_tag_id]['items'] = sequence_description
current_descriptions[-1][last_tag_id][
'items'] = sequence_description
current_descriptions.append(sequence_description)
except KeyError:
# silently ignore error in older specs
Expand All @@ -227,12 +248,15 @@ def _get_tag_name_and_level(self, column, current_descriptions, current_level, l
return tag_name, level

def _get_iod_modules(self, iod_node):
module_table_sections = self._find_sections_with_title_endings(iod_node, (' Module Table', ' IOD Modules'))
module_table_sections = self._find_sections_with_title_endings(
iod_node, (' Module Table', ' IOD Modules'))
if not module_table_sections:
module_table_sections = self._find_sections_with_title_endings(iod_node, ('IOD Entity-Relationship Model',))
module_table_sections = self._find_sections_with_title_endings(
iod_node, ('IOD Entity-Relationship Model',))
modules = {}
if len(module_table_sections) == 1:
module_rows = self._findall(module_table_sections[0], ['table', 'tbody', 'tr'])
module_rows = self._findall(module_table_sections[0],
['table', 'tbody', 'tr'])
row_span = 0
for row in module_rows:
columns = self._findall(row, ['td'])
Expand All @@ -245,19 +269,26 @@ def _get_iod_modules(self, iod_node):
name = self._find_text(columns[name_index])
modules[name] = {}
try:
ref_section = self._find(columns[name_index + 1], ['para', 'xref']).attrib['linkend'].split('_')[1]
ref_section = self._find(columns[name_index + 1],
['para', 'xref']).attrib[
'linkend'].split('_')[1]
except AttributeError:
try:
ref_section = self._find(columns[name_index + 1], ['xref']).attrib['linkend'].split('_')[1]
ref_section = self._find(
columns[name_index + 1], ['xref']).attrib[
'linkend'].split('_')[1]
except AttributeError:
self.logger.warning('Failed to read module table for %s', name)
self.logger.warning(
'Failed to read module table for %s', name)
continue
modules[name]['ref'] = ref_section
# make sure the module description is loaded
self.module_description(ref_section)
modules[name]['use'] = self._find_text(columns[name_index + 2])
if self._condition_parser is not None and modules[name]['use'].startswith('C - '):
modules[name]['cond'] = self._condition_parser.parse(modules[name]['use'])
if (self._condition_parser is not None and
modules[name]['use'].startswith('C - ')):
modules[name]['cond'] = self._condition_parser.parse(
modules[name]['use'])
else:
modules[name]['use'] = modules[name]['use'][0]
row_span -= 1
Expand All @@ -270,6 +301,7 @@ def _find_sections_with_title_endings(self, node, title_endings):
title_node = self._find(sections_node, ['title'])
if title_node is not None:
title = title_node.text
if any([title.endswith(title_ending) for title_ending in title_endings]):
if any([title.endswith(title_ending) for title_ending in
title_endings]):
found_nodes.append(sections_node)
return found_nodes
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