Update standard to rev2024b

- Add new workarounds
- Update tests

README.md

@@ -112,12 +112,16 @@ significantly.
 ### Updating the Standard
 
 To download and parse the most up-to-date web version of the DICOM Standard,
-run the following commands:
+run the following commands in the `dicom_standard` directory:
 
     $ make clean
     $ make updatestandard
     $ make
 
+Then copy the output to the `standard/` directory:
+
+    $ cp dist/* ../standard/
+
 To download an older version of the DICOM Standard, run
 
     $ make updatestandard VERSION=<version>
@@ -236,7 +240,7 @@ Certain parts of the DICOM Standard site cause errors when running the parser, o
 
 When we find one of these issues, we add a hard-coded fix in the relevant file and add a comment starting with 'Standard workaround' that describes the issue and links to its location in the Standard. To be aware when these fixes are obsolete, we add a unit test that fails once the issue no longer exists.
 
-Current standard workarounds (as of rev.2023e):
+Current standard workarounds (as of rev.2024b):
 | *Issue description* | *Workaround location* |
 |---|---|
 | [Table TID 1004](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_A.html#sect_TID_1004) has a section URL pattern ("sect_TID_1004") that doesn't exist within the HTML version of the standard | `parse_lib.py` |
@@ -247,6 +251,9 @@ Current standard workarounds (as of rev.2023e):
 | The "Referenced Patient Alias Sequence" attribute is noted to be retired in [Table 6-1](https://dicom.nema.org/medical/dicom/current/output/chtml/part06/chapter_6.html#para_74d743fc-e532-4817-8477-58d1e9a8de57) but is not retired in [Table E.1-1](https://dicom.nema.org/medical/dicom/current/output/html/part15.html#para_26d0b4be-9dae-4b57-ab18-8e524dde7dc1) | `extract_conf_profile_attributes.py` |
 | The [Confocal Microscopy Image Functional Group Macros](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.90.html#sect_A.90.1.5) section doesn't have a description, causing the "module_type" value to be None when it should be "Multi-frame" | `extract_ciod_func_group_macro_tables.py` |
 | The [Confocal Microscopy Tiled Pyramidal Image Functional Group Macros](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.90.2.5.html#sect_A.90.2.5) section doesn't have a description, causing the "module_type" value to be None when it should be "Multi-frame" | `extract_ciod_func_group_macro_tables.py` |
+| [Table A.89.4-1](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.89.4.html#table_A.89.4-1) is missing part of the IOD name ("Photoacoustic" instead of "Photoacoustic Image") in its title | `extract_ciod_func_group_macro_tables.py` |
+| The "Confocal Micrsocopy Tiled Pyramidal" IOD Specification in [Table B.5-1](https://dicom.nema.org/medical/dicom/current/output/chtml/part04/sect_B.5.html#table_B.5-1) should include the word "Image" after "Pyramidal" | `extract_sops.py`
+| The "Pseudo-color Softcopy Presentation State" IOD Specification in [Table B.5-1](https://dicom.nema.org/medical/dicom/current/output/chtml/part04/sect_B.5.html#table_B.5-1) should have an upper-case "C" in "Color" | `extract_sops.py`
 
 (\*) This issue is not caused by a typo or error in the Standard but rather an exception from the normal format and thus does not have a unit test for a fix.
 

dicom_standard/extract_ciod_func_group_macro_tables.py

@@ -28,10 +28,10 @@
 
 def clean_macro_table_name(table_name: str) -> str:
     clean_name = pl.clean_table_name(table_name)
-    # Standard workaround: Mismatch of 'Photoacoustic Reconstruction Algorithm' name
+    # Standard workaround: Table A.89.4-1 is missing part of the IOD name ("Photoacoustic" instead of "Photoacoustic Image") in its title
     # https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.89.4.html#table_A.89.4-1
-    if clean_name == 'Photoacoustic Reconstruction Algorithm Macro Attributes':
-        clean_name = 'Photoacoustic Reconstruction Algorithm'
+    if clean_name == 'Photoacoustic':
+        clean_name = 'Photoacoustic Image'
     return clean_name
 
 
@@ -56,7 +56,7 @@ def get_table_with_metadata(table_with_tdiv: Tuple[List[TableDictType], Tag]) ->
     # https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.90.2.5.html#sect_A.90.2.5
     # https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.90.html#para_432a2653-f9c3-474e-829b-3997312e0ecd
     # Example valid section: https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.8.3.5.html
-    if clean_name == "Confocal Microscopy Image" or clean_name == "Confocal Microscopy Tiled Pyramidal Image":
+    if clean_name == 'Confocal Microscopy Image' or clean_name == 'Confocal Microscopy Tiled Pyramidal Image':
         module_type = 'Multi-frame'
     return {
         'name': clean_name,

dicom_standard/extract_sops.py

@@ -6,25 +6,19 @@
 
 COLUMN_TITLES = ['name', 'id', 'ciod']
 TABLE_IDS = ['table_B.5-1', 'table_I.4-1', 'table_GG.3-1']
-IOD_ABBREVIATIONS = {
-    'Computed Radiography Image': 'CR Image',
-    'Ultrasound Multi-frame Image': 'US Multi-frame Image',
-    'Ultrasound Image': 'US Image',
-    'Multi-frame Single Bit Secondary Capture Image': 'Multi-frame Single Bit SC Image',
-    'Multi-frame Grayscale Byte Secondary Capture Image': 'Multi-frame Grayscale Byte SC Image',
-    'Multi-frame Grayscale Word Secondary Capture Image': 'Multi-frame Grayscale Word SC Image',
-    'Multi-frame True Color Secondary Capture Image': 'Multi-frame True Color SC Image',
-    'Pseudo-color Softcopy Presentation State': 'Pseudo-Color Softcopy Presentation State',
-    'Intravascular Optical Coherence Tomography': 'Intravascular Optical Coherence Tomography Image',  # Inconsistent name: http://dicom.nema.org/medical/Dicom/current/output/chtml/part03/sect_A.66.html
-    'Nuclear Medicine Image': 'NM Image',
-    'Patient Radiation Dose SR': 'Patient Radiation Dose Structured Report',
-    'Positron Emission Tomography Image': 'PET Image',
-}
 
 
 def generate_ciod_id(name: str) -> str:
     cleaned_name = name.split('IOD')[0].strip()
-    return IOD_ABBREVIATIONS.get(cleaned_name, cleaned_name)
+    # Standard workaround: Table B.5-1 is missing part of the IOD name ("Confocal Microscopy Tiled Pyramidal" instead of "Confocal Microscopy Tiled Pyramidal Image")
+    # https://dicom.nema.org/medical/dicom/current/output/chtml/part04/sect_B.5.html#table_B.5-1
+    if cleaned_name == 'Confocal Microscopy Tiled Pyramidal':
+        cleaned_name = 'Confocal Microscopy Tiled Pyramidal Image'
+    # Standard workaround: Table B.5-1 has a miscapitalized word in an IOD Specification
+    # https://dicom.nema.org/medical/dicom/current/output/chtml/part04/sect_B.5.html#table_B.5-1
+    if cleaned_name == 'Pseudo-color Softcopy Presentation State':
+        cleaned_name = 'Pseudo-Color Softcopy Presentation State'
+    return cleaned_name
 
 
 def sop_table_to_json(table: List[TableDictType]) -> List[TableDictType]:

dicom_standard/parse_lib.py

@@ -85,11 +85,6 @@ def clean_table_name(name: str) -> str:
     _, _, title = re.split('\u00a0', name)
     possible_table_suffixes = r'(IOD Modules)|(Module Attributes)|((Functional Group)? Macro Attributes)|(Module Table)|(Functional Group Macros)'
     clean_title = re.split(possible_table_suffixes, title)[0]
-    # Standard workaround: Macro table name 'Photoacoustic Reconstruction Algorithm Attributes',
-    # which is not following the normal format
-    # https://dicom.nema.org/medical/dicom/2023c/output/chtml/part03/sect_A.89.4.html#table_A.89.4-1
-    if clean_title == 'Photoacoustic Reconstruction Algorithm Attributes':
-        clean_title = 'Photoacoustic Reconstruction Algorithm'
     return clean_title.strip()