Merge pull request #35 from innolitics/16-functional-group-macros

Process Functional Group Macros

dicom_standard/Makefile

@@ -1,4 +1,5 @@
-.SUFFIXES:)
+.SUFFIXES:
+.DELETE_ON_ERROR:
 
 .PHONY: clean tests unittest endtoendtest updatestandard checkversions
 
@@ -21,8 +22,8 @@ relationship_tables: dist/ciod_to_modules.json dist/ciod_to_func_group_macros.js
 dist/ciods.json: tmp/raw_ciod_module_tables.json
 	$(PYTHONPATH_PREFIX) python3 process_ciods.py $< > $@
 
-dist/modules.json: tmp/preprocessed_modules_attributes.json
-	$(PYTHONPATH_PREFIX) python3 process_modules.py $< > $@
+dist/modules.json: tmp/preprocessed_modules_attributes.json dist/ciod_to_func_group_macros.json
+	$(PYTHONPATH_PREFIX) python3 process_modules.py $^ > $@
 
 dist/macros.json: tmp/preprocessed_macros_attributes.json
 	$(PYTHONPATH_PREFIX) python3 process_macros.py $< > $@
@@ -42,8 +43,8 @@ dist/ciod_to_modules.json: tmp/raw_ciod_module_tables.json
 dist/ciod_to_func_group_macros.json: tmp/raw_ciod_func_group_macro_tables.json
 	$(PYTHONPATH_PREFIX) python3 process_ciod_func_group_macro_relationship.py $< > $@
 
-dist/module_to_attributes.json: tmp/modules_attributes_updated_references.json
-	$(PYTHONPATH_PREFIX) python3 postprocess_merge_duplicate_nodes.py $< > $@
+dist/module_to_attributes.json: tmp/module_to_attributes_no_duplicates.json dist/macros.json dist/ciod_to_func_group_macros.json dist/macro_to_attributes.json
+	$(PYTHONPATH_PREFIX) python3 postprocess_integrate_func_group_macros.py $^ > $@
 
 dist/macro_to_attributes.json: tmp/macros_attributes_partial_references.json dist/references.json
 	$(PYTHONPATH_PREFIX) python3 postprocess_update_reference_links.py $^ > $@
@@ -52,6 +53,9 @@ dist/references.json: tmp/modules_attributes_partial_references.json tmp/raw_sec
 	$(PYTHONPATH_PREFIX) python3 postprocess_save_references.py $^ > $@
 
 
+tmp/module_to_attributes_no_duplicates.json: tmp/modules_attributes_updated_references.json
+	$(PYTHONPATH_PREFIX) python3 postprocess_merge_duplicate_nodes.py $< > $@
+
 tmp/modules_attributes_updated_references.json: tmp/modules_attributes_partial_references.json dist/references.json
 	$(PYTHONPATH_PREFIX) python3 postprocess_update_reference_links.py $^ > $@
 

dicom_standard/extract_ciod_func_group_macro_tables.py

@@ -5,6 +5,7 @@
 from typing import List, Tuple
 import sys
 import re
+from copy import deepcopy
 
 from bs4 import Tag
 
@@ -58,8 +59,22 @@ def get_table_with_metadata(table_with_tdiv: Tuple[List[TableDictType], Tag]) ->
     }
 
 
+def add_enhanced_mr_color_image_table(table_data):
+    ''' Standard workaround: The Enhanced MR Color Image IOD does not have its own set
+    of Functional Group Macros, but instead refers to the Enhanced MR Image Functional
+    Group Macros Table, so we duplicate that table object and modify the name
+    See http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.36.4.4.html
+    '''
+    enhanced_mr_image_fg_macros = next(filter(lambda t: t['name'] == 'Enhanced MR Image', table_data), None)
+    assert enhanced_mr_image_fg_macros is not None, 'Table with name "Enhanced MR Image" not found.'
+    new_table = deepcopy(enhanced_mr_image_fg_macros)
+    new_table['name'] = 'Enhanced MR Color Image'
+    table_data.append(new_table)
+
+
 if __name__ == "__main__":
     standard = pl.parse_html_file(sys.argv[1])
     tables, tdivs = get_chapter_tables(standard, CHAPTER_ID, is_valid_macro_table)
     parsed_table_data = tables_to_json(tables, tdivs, macro_table_to_dict, get_table_with_metadata)
+    add_enhanced_mr_color_image_table(parsed_table_data)
     pl.write_pretty_json(parsed_table_data)

dicom_standard/postprocess_integrate_func_group_macros.py

@@ -0,0 +1,68 @@
+'''
+Add functional group macro attributes to module_to_attributes.json
+'''
+import sys
+from copy import deepcopy
+
+import dicom_standard.parse_lib as pl
+from dicom_standard.process_modules import FUNC_GROUP_MODULE_ID
+
+PER_FRAME_FUNC_GROUP_ID = 52009230
+
+
+def update_description(attribute, macro):
+    note_header = '<h3>Note</h3>'
+    usage = f'<p>Part of the {macro["macroName"]} Functional Group Macro with usage: {macro["usage"]}</p>'
+    conditionalStatement = macro['conditionalStatement']
+    if conditionalStatement and not conditionalStatement.endswith('.'):
+        conditionalStatement += '.'
+    conditional = f'<p>{conditionalStatement}</p>' if conditionalStatement else ''
+    attribute['description'] += note_header + usage + conditional
+
+
+def process_macro_attributes(macro_attrs, macro):
+    attr_list = []
+    for macro_attr in macro_attrs:
+        attr = deepcopy(macro_attr)
+        macro_id = attr.pop('macroId')
+        attr['moduleId'] = f'{macro["ciodId"]}-{FUNC_GROUP_MODULE_ID}'
+        new_path_prefix = f'{attr["moduleId"]}:{PER_FRAME_FUNC_GROUP_ID}'
+        attr['path'] = attr['path'].replace(macro_id, new_path_prefix)
+        update_description(attr, macro)
+        attr_list.append(attr)
+    return attr_list
+
+
+def process_mffg_attributes(ciods, mffg_attrs):
+    attr_list = []
+    for ciod in ciods:
+        module_id = f'{ciod}-{FUNC_GROUP_MODULE_ID}'
+        for mffg_attr in mffg_attrs:
+            attr = deepcopy(mffg_attr)
+            attr['moduleId'] = module_id
+            attr['path'] = attr['path'].replace(FUNC_GROUP_MODULE_ID, module_id)
+            attr_list.append(attr)
+    return attr_list
+
+
+def process_ciod_specific_attributes(module_to_attr, macros, ciod_to_macro, macro_to_attr):
+    ciod_specific_attrs = []
+    macro_dict = {macro['id']: macro for macro in macros}
+    for rel in ciod_to_macro:
+        rel['macroName'] = macro_dict[rel['macroId']]['name']
+        macro_attrs = list(filter(lambda r: r['macroId'] == rel['macroId'], macro_to_attr))
+        processed_macro_attrs = process_macro_attributes(macro_attrs, rel)
+        ciod_specific_attrs += processed_macro_attrs
+    mffg_attrs = list(filter(lambda r: r['moduleId'] == FUNC_GROUP_MODULE_ID, module_to_attr))
+    ciods_with_macros = list(set([rel['ciodId'] for rel in ciod_to_macro]))
+    ciod_specific_attrs += process_mffg_attributes(ciods_with_macros, mffg_attrs)
+    return ciod_specific_attrs
+
+
+if __name__ == '__main__':
+    module_to_attributes = pl.read_json_data(sys.argv[1])
+    macros = pl.read_json_data(sys.argv[2])
+    ciod_to_macro = pl.read_json_data(sys.argv[3])
+    macro_to_attributes = pl.read_json_data(sys.argv[4])
+    new_attributes = process_ciod_specific_attributes(module_to_attributes, macros, ciod_to_macro, macro_to_attributes)
+    pl.write_pretty_json(module_to_attributes + new_attributes)

dicom_standard/preprocess_modules_with_attributes.py

@@ -15,10 +15,7 @@
 
 
 def key_tables_by_id(table_list: List[MetadataTableType]) -> Dict[str, MetadataTableType]:
-    dict_of_tables = {}
-    for table in table_list:
-        dict_of_tables[get_id_from_link(table['linkToStandard'])] = table
-    return dict_of_tables
+    return {get_id_from_link(table['linkToStandard']): table for table in table_list}
 
 
 def expand_all_macros(module_attr_tables, macros):

dicom_standard/process_ciod_module_relationship.py

@@ -39,9 +39,14 @@ def define_ciod_module_relationship(ciod, module):
             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']))
+    # Add CIOD ID to differentiate "Multi-Frame Functional Group" modules for different CIODs
+    if module_id == 'multi-frame-functional-groups':
+        module_id = f'{ciod_id}-{module_id}'
     return {
-        "ciodId": pl.create_slug(ciod),
-        "moduleId": pl.create_slug(pl.text_from_html_string(module['module'])),
+        "ciodId": ciod_id,
+        "moduleId": module_id,
         "usage": usage,
         "conditionalStatement": conditional_statement,
         "informationEntity": information_entity,

dicom_standard/process_modules.py

@@ -2,9 +2,14 @@
 Convert the processed module-attribute JSON data into a
 normalized listing of all modules in the DICOM Standard.
 '''
+from typing import cast, List
 import sys
+from copy import deepcopy
 
 from dicom_standard import parse_lib as pl
+from dicom_standard.macro_utils import MetadataTableType
+
+FUNC_GROUP_MODULE_ID = 'multi-frame-functional-groups'
 
 
 def modules_from_tables(tables):
@@ -17,7 +22,21 @@ def modules_from_tables(tables):
     return modules
 
 
+def create_ciod_specific_modules(ciods, mffg_module):
+    modules = []
+    for ciod in ciods:
+        ciod_specific_module = deepcopy(mffg_module)
+        ciod_specific_module['id'] = f'{ciod}-{FUNC_GROUP_MODULE_ID}'
+        modules.append(ciod_specific_module)
+    return modules
+
+
 if __name__ == '__main__':
     module_attr_tables = pl.read_json_data(sys.argv[1])
+    ciod_to_macro = cast(List[MetadataTableType], pl.read_json_data(sys.argv[2]))
     modules = modules_from_tables(module_attr_tables)
-    pl.write_pretty_json(modules)
+    ciods_with_macros = list(set([rel['ciodId'] for rel in ciod_to_macro]))
+    multi_frame_func_group_module = next(filter(lambda rel: rel['id'] == FUNC_GROUP_MODULE_ID, modules), None)
+    assert multi_frame_func_group_module is not None, f'Module ID "{FUNC_GROUP_MODULE_ID}" not found in modules.json'
+    ciod_specific_modules = create_ciod_specific_modules(ciods_with_macros, multi_frame_func_group_module)
+    pl.write_pretty_json(modules + ciod_specific_modules)

standard/ciod_to_func_group_macros.json

@@ -2194,5 +2194,179 @@
         "macroId":"real-world-value-mapping",
         "usage":"U",
         "conditionalStatement":null
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"pixel-measures",
+        "usage":"M",
+        "conditionalStatement":null
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"frame-content",
+        "usage":"M",
+        "conditionalStatement":null
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"plane-position-patient",
+        "usage":"M",
+        "conditionalStatement":null
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"plane-orientation-patient",
+        "usage":"M",
+        "conditionalStatement":null
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"referenced-image",
+        "usage":"C",
+        "conditionalStatement":"Required if the image or frame has been planned on another image or frame. May be present otherwise"
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"derivation-image",
+        "usage":"C",
+        "conditionalStatement":"Required if the image or frame has been derived from another SOP Instance."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"cardiac-synchronization",
+        "usage":"C",
+        "conditionalStatement":"Required if Cardiac Synchronization Technique (0018,9037) equals other than NONE and if Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"frame-anatomy",
+        "usage":"M",
+        "conditionalStatement":null
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"pixel-value-transformation",
+        "usage":"C",
+        "conditionalStatement":"Required if Photometric Interpretation (0028,0004) is MONOCHROME2."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"frame-voi-lut",
+        "usage":"U",
+        "conditionalStatement":null
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"real-world-value-mapping",
+        "usage":"U",
+        "conditionalStatement":null
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"contrast-bolus-usage",
+        "usage":"C",
+        "conditionalStatement":"Required if Contrast/Bolus Agent Sequence (0018,0012) is used."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"respiratory-synchronization",
+        "usage":"C",
+        "conditionalStatement":"Required if Respiratory Motion Compensation Technique (0018,9170) equals other than NONE, REALTIME or BREATH_HOLD and if Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-image-frame-type",
+        "usage":"M",
+        "conditionalStatement":null
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-timing-and-related-parameters",
+        "usage":"C",
+        "conditionalStatement":"Required if Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-fov-geometry",
+        "usage":"C",
+        "conditionalStatement":"Required if Geometry of k-Space Traversal (0018,9032) equals RECTILINEAR and if Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-echo",
+        "usage":"C",
+        "conditionalStatement":"Required if Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-modifier",
+        "usage":"C",
+        "conditionalStatement":"Required if Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-imaging-modifier",
+        "usage":"C",
+        "conditionalStatement":"Required if Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-receive-coil",
+        "usage":"C",
+        "conditionalStatement":"Required if Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-transmit-coil",
+        "usage":"C",
+        "conditionalStatement":"Required if Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-diffusion",
+        "usage":"C",
+        "conditionalStatement":"Required if Acquisition Contrast (0008,9209) in any MR Image Frame Type Functional Group in the SOP Instance equals DIFFUSION and Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-averages",
+        "usage":"C",
+        "conditionalStatement":"Required if Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-spatial-saturation",
+        "usage":"C",
+        "conditionalStatement":"Required if Spatial Pre-saturation (0018,9027) equals SLAB for any frame in the SOP Instance and Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-metabolite-map",
+        "usage":"C",
+        "conditionalStatement":"Required if Image Type (0008,0008) Value 3 equals METABOLITE_MAP. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-velocity-encoding",
+        "usage":"C",
+        "conditionalStatement":"Required if Phase Contrast (0018,9014) equals YES and Image Type (0008,0008) Value 1 is ORIGINAL or MIXED. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"mr-arterial-spin-labeling",
+        "usage":"C",
+        "conditionalStatement":"Required if Image Type (0008,0008) Value 3 is ASL. May be present otherwise."
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"functional-mr",
+        "usage":"U",
+        "conditionalStatement":null
+    },
+    {
+        "ciodId":"enhanced-mr-color-image",
+        "macroId":"temporal-position",
+        "usage":"U",
+        "conditionalStatement":null
     }
 ]