dcmspec 0.2.1__py3-none-any.whl

dcmspec/apps/cli/tdwiicontent.py

@@ -0,0 +1,365 @@
+"""CLI for extracting and printing the TDW-II content specifications from the IHE-RO Supplement.
+
+IHE profiles define additional requirements for DICOM Services and Objects.
+IOD specifications (which modules are required for each IOD) are defined in section 7.3, "IOD Definitions."
+Module specifications (which attributes are defined within each module) are found in section 7.4, "Module Definitions."
+In IHE-RO profiles, module specifications are organized into two parts:
+- a base definition, which applies to all transactions or content definitions where the module is used
+- an extension, which applies only to a particular transaction or content definition.
+
+This CLI tool focuses on the IHE-RO TDW-II workflow profile and extract the content definitions relevant to each 
+transaction.
+
+Features:
+- Download and parse TDW-II module base and extension definition tables from the IHE-RO Supplement in PDF format.
+- Extract and print the module definition as a table and a tree.
+- Cache the resulting model as a JSON file for future runs and as a structured representation of the table.
+- Supports configuration, caching, and command-line options for flexible workflows.
+
+Usage:
+    poetry run python -m src.dcmspec.apps.cli.tdwiimoddefinition [options]
+
+For more details, use the --help option.
+"""
+
+import argparse
+from copy import deepcopy
+import logging
+
+from anytree import Node
+
+from dcmspec.json_spec_store import JSONSpecStore
+from dcmspec.pdf_doc_handler import PDFDocHandler
+from dcmspec.csv_table_spec_parser import CSVTableSpecParser
+from dcmspec.spec_factory import SpecFactory
+from dcmspec.spec_model import SpecModel
+from dcmspec.spec_printer import SpecPrinter
+
+# Configurations for each content definition
+CONTENT_DEFINITION_CONFIGS = {
+    "ups_scheduled": {
+        "page_numbers": [57, 58],
+        "table_indices": [(57, 1), (58, 0)],
+        "table_id": "tdwii_ups_scheduled_info",
+        "column_to_attr": {0: "elem_name", 1: "elem_tag", 2: "elem_type", 3: "elem_description"},
+    },
+    "ups_performed": {
+        "page_numbers": [61, 62],
+        "table_indices": [(61, 0), (62, 0)],
+        "table_id": "tdwii_ups_performed_info",
+        "column_to_attr": {0: "elem_name", 1: "elem_tag", 2: "elem_type", 3: "elem_description"},
+    },
+    "ups_progress": {
+        "page_numbers": [64],
+        "table_indices": [(64,0)],
+        "table_header_rowspan": {(64,0): 1},
+        "table_id": "tdwii_ups_progress_info",
+        "column_to_attr": {0: "elem_name", 1: "elem_tag", 2: "elem_type", 3: "elem_description"},
+    },
+    "ups_relationship": {
+        "page_numbers": [60],
+        "table_indices": [(60, 1)],
+        "table_id": "tdwii_ups_relationship_info",
+        "column_to_attr": {0: "elem_name", 1: "elem_tag", 2: "elem_type", 3: "elem_description"},
+    },
+    "ups_query": {
+        "page_numbers": [63],
+        "table_indices": [(63, 0)],
+        "table_header_rowspan": {(63, 0): 2},
+        "table_id": "tdwii_ups_query_info",
+        "column_to_attr": {
+            0: "elem_name",
+            1: "elem_tag",
+            2: "key_matching_scu",
+            3: "key_matching_scp",
+            4: "key_return_scu",
+            5: "key_return_scp",
+        },
+    },
+    "rt_bdi": {
+        "page_numbers": [55, 56, 57],
+        "table_indices": [(55, 1), (56, 0), (57, 0)],
+        "table_id": "tdwii_bdi_instruction_info",
+        "column_to_attr": {0: "elem_name", 1: "elem_tag", 2: "elem_type", 3: "elem_description"},
+    },
+}
+
+def _extract_module_definition(
+    pdf_file,
+    url,
+    page_numbers,
+    table_indices,
+    table_header_rowspan,
+    table_id,
+    column_to_attr,
+    logger,
+    force_parse=False,
+):
+    """Extract and return the TDW-II module definition model."""
+    factory = SpecFactory(
+        input_handler=PDFDocHandler(logger=logger, extractor="pdfplumber"),
+        table_parser=CSVTableSpecParser(logger=logger),
+        column_to_attr=column_to_attr,
+        name_attr="elem_name",
+        logger=logger
+    )
+
+    handler_kwargs = {
+        "page_numbers": page_numbers,
+        "table_indices": table_indices,
+        "table_header_rowspan": table_header_rowspan,
+        "table_id": table_id,
+    }
+
+    return factory.create_model(
+        url=url,
+        cache_file_name=pdf_file,
+        table_id=table_id,
+        force_parse=force_parse,
+        json_file_name=f"{table_id}.json",
+        handler_kwargs=handler_kwargs,
+    )
+
+def _parse_args():
+    """Parse and return command-line arguments for the TDW-II CLI."""
+    parser = argparse.ArgumentParser(description="Extract and print TDW-II UPS module information tables.")
+    parser.add_argument(
+        "content_definition",
+        choices=[
+            "ups_create",
+            "ups_performed",
+            "ups_progress",
+            "ups_query",
+            "rt_bdi"
+            # Add more content_definition names here as you add configs
+        ],
+        help=(
+            "Select which content definition to extract: "
+            "'ups_create', 'ups_query', 'ups_progress', 'ups_performed', 'rt_bdi'"
+        )
+    )
+    parser.add_argument("-d", "--debug", action="store_true", help="Enable debug logging")
+    parser.add_argument("-v", "--verbose", action="store_true", help="Enable verbose output")
+    return parser.parse_args()
+
+def _setup_logger(debug=False, verbose=False):
+    """Set up and return a logger with the appropriate log level."""
+    if debug:
+        log_level = logging.DEBUG
+    elif verbose:
+        log_level = logging.INFO
+    else:
+        log_level = logging.WARNING
+
+    logging.basicConfig(
+        level=log_level,
+        format="%(asctime)s - %(levelname)s - %(message)s"
+    )
+
+    # Suppress PDFMiner debug logs
+    logging.getLogger("pdfminer").setLevel(logging.WARNING)
+
+    logger = logging.getLogger("tdwiimoddefinition")
+    logger.setLevel(log_level)  # <-- This ensures the logger is always at the correct level
+
+    return logger
+
+def _extract_ups_create_model(pdf_file, url, logger):
+    """Extract and combine UPS Scheduled and Relationship module definition."""
+    base_config = CONTENT_DEFINITION_CONFIGS["ups_scheduled"]
+    base_config_part2 = CONTENT_DEFINITION_CONFIGS["ups_relationship"]
+
+    scheduled_model = _extract_module_definition(
+        pdf_file=pdf_file,
+        url=url,
+        page_numbers=base_config["page_numbers"],
+        table_indices=base_config["table_indices"],
+        table_header_rowspan=base_config.get("table_header_rowspan", None),
+        table_id=base_config["table_id"],
+        column_to_attr=base_config["column_to_attr"],
+        logger=logger,
+        force_parse=False,
+    )
+    relationship_model = _extract_module_definition(
+        pdf_file=pdf_file,
+        url=url,
+        page_numbers=base_config_part2["page_numbers"],
+        table_indices=base_config_part2["table_indices"],
+        table_header_rowspan=base_config.get("table_header_rowspan", None),
+        table_id=base_config_part2["table_id"],
+        column_to_attr=base_config_part2["column_to_attr"],
+        logger=logger,
+        force_parse=False,
+    )
+    # Combine the two models under a new root node
+    combined_root = Node("content")
+    # Attach all children of scheduled_model.content
+    for child in list(scheduled_model.content.children):
+        child.parent = combined_root
+    # Attach all children of relationship_model.content
+    for child in list(relationship_model.content.children):
+        child.parent = combined_root
+
+    # Use metadata from scheduled_model, but set a new table_id for the combined model
+    combined_metadata = deepcopy(scheduled_model.metadata)
+    combined_metadata.table_id = "tdwii_ups_create_info"
+    return SpecModel(
+        metadata=combined_metadata,
+        content=combined_root,
+        logger=logger,
+    )
+
+def _apply_hard_coded_extensions(model, content_definition_name):
+    """Apply hard-coded extensions to the base model for specific modules."""
+    for node in model.content.children:
+        elem_name = getattr(node, "elem_name", "").strip()
+
+        if content_definition_name == "ups_create":
+            if elem_name == "Scheduled Workitem Code Sequence":
+                for child in node.children:
+                    child_name = getattr(child, "elem_name", "").strip()
+                    if child_name == ">Code Value":
+                        child.elem_description = 'shall be equal to "121726"'
+                    elif child_name == ">Coding Scheme Designator":
+                        child.elem_description = 'shall be equal to "DCM"'
+                    elif child_name == ">Code Meaning":
+                        child.elem_description = 'shall be equal to "RT Treatment with Internal Verification"'
+                continue
+            if elem_name == "Input Information Sequence":
+                node.elem_description = (
+                    "Shall contain at least 2 Referenced DICOM Instances:"
+                    "\nRT Plan Storage or RT Ion Plan Storage retrieved from OST."
+                    "\nRT Beams Delivery Instruction Storage retrieved from TMS."
+                    "\nShall contain more Referenced DICOM Instances if Treatment Delivery Type is equal to "
+                    "CONTINUATION:"
+                    "\nRT Beams Treatment Record Storage or RT Ion Beams Treatment Record Storage retrieved from OST."
+                    "\nMay contain additional items for other reasons, which are out of scope for this profile"
+                )
+                continue
+            if elem_name == "Scheduled Processing Parameters Sequence":
+                node.elem_description = (
+                    "Shall include 4 Content Items per Template:"
+                    '\nEV (121740, DCM, "Treatment Delivery Type"), VT:TEXT (TREAMENT or CONTINUATION).'
+                    '\nEV (2018001, 99IHERO2018, "Plan Label"), VT:TEXT (RT Plan Label (300A,0002) value).'
+                    '\nEV (2018002, 99IHERO2018, "Current Fraction Number"), VT:NUMERIC '
+                    "(Current Fraction Number (3008,0022) value)."
+                    '\nEV (2018003, 99IHERO2018, "Number of Fractions Planned"), VT:NUMERIC '
+                    "(Number of Fractions Planned (300A,0078) value)."
+                )
+                continue
+
+        if content_definition_name == "ups_performed":
+            if elem_name == ">Performed Workitem Code Sequence":
+                for child in node.children:
+                    child_name = getattr(child, "elem_name", "").strip()
+                    if child_name == ">Code Value":
+                        child.elem_description = 'shall be equal to "121726"'
+                    elif child_name == ">Coding Scheme Designator":
+                        child.elem_description = 'shall be equal to "DCM"'
+                    elif child_name == ">Code Meaning":
+                        child.elem_description = 'shall be equal to "RT Treatment with Internal Verification"'
+                continue
+            if elem_name == ">Output Information Sequence":
+                node.elem_description = (
+                    "Shall contain at least 1 item if any therapeutic treatment was delivered to the patient:"
+                    "\nRT Beams Treatment Record Storage (1.2.840.10008.5.1.4.1.1.481.4) or "
+                    "RT Ion Beams Treatment Record Storage (1.2.840.10008.5.1.4.1.1.481.9) stored to OST."
+                    "\nMay be present otherwise."
+                )
+                continue
+
+        if content_definition_name == "ups_progress" and elem_name == "Procedure Step Progress Information Sequence":
+            # Add missing Procedure Step Progress Parameters Sequence to the model
+            Node(
+                "procedure_step_progress_parameters_sequence",
+                parent=node,
+                elem_name=">Procedure Step Progress Parameters Sequence",
+                elem_tag="(0074,1007)",
+                elem_type="R+*",
+                elem_description=(
+                    "Shall include 1 Content Item per Template:"
+                    '\nEV (2018004, 99IHERO2018, "Referenced Beam Number"), VT:NUM '
+                    "(Beam Number (300A,00C0) value of beam in progress)."
+                ),
+            )
+            continue
+
+def main():
+    """CLI for extracting and printing the TDW-II Content Definitions from the IHE-RO Supplement.
+
+    This CLI downloads, parses, and prints the TDW-II Content Definitions from the IHE-RO Supplement (PDF).
+    The tool extracts the relevant table(s) from the PDF, parses the content definition, and outputs the result as a
+    table and a tree.
+
+    The resulting model is cached as a JSON file. The primary purpose of this cache file is to provide a structured,
+    machine-readable representation of the content definition, which can be used for further processing or integration
+    in other tools. As a secondary benefit, the cache file is also used to speed up subsequent runs of the CLI scripts.
+
+    Usage:
+        poetry run python -m src.dcmspec.apps.cli.tdwiicontent <content_definition> [options]
+
+        Where <content_definition> is one of:
+        - ups_create: content of scheduled UPS creation (combined UPS Scheduled and Relationship definitions).
+        - ups_query: content of C-FIND identifier for UPS Query transaction.
+        - ups_progress: content of N-SET dataset for UPS Progress Update transaction.
+        - ups_performed: content of N-SET dataset for UPS Final Status Update transaction.
+        - rt_bdi: content of RT Beam Delivery Instruction Module.
+
+    Options:
+        -d, --debug: Enable debug logging.
+        -v, --verbose: Enable verbose output.
+
+    Example:
+        poetry run python -m src.dcmspec.apps.cli.tdwiicontent ups_progress --debug
+
+    For more details, use the --help option.
+
+    """
+    args = _parse_args()
+    logger = _setup_logger(debug=args.debug, verbose=args.verbose)
+
+    logger.info(f"Extracting TDW-II module definition for: {args.content_definition}")
+    logger.debug(f"Arguments: {args}")
+
+    # TDW-II Supplement PDF and URL (shared for all module extractions)
+    pdf_file = "IHE_RO_Suppl_TDW_II.pdf"
+    url = "https://www.ihe.net/uploadedFiles/Documents/Radiation_Oncology/IHE_RO_Suppl_TDW_II.pdf"
+
+    # Special handling for ups_create: combine ups_scheduled and ups_relationship models
+    if args.content_definition == "ups_create":
+        base_model = _extract_ups_create_model(pdf_file, url, logger)
+    else:
+        # Select config based on argument
+        base_config = CONTENT_DEFINITION_CONFIGS[args.content_definition]
+
+        # Extract base and extension models
+        base_model = _extract_module_definition(
+            pdf_file=pdf_file,
+            url=url,
+            page_numbers=base_config["page_numbers"],
+            table_indices=base_config["table_indices"],
+            table_header_rowspan=base_config.get("table_header_rowspan", None),
+            table_id=base_config["table_id"],
+            column_to_attr=base_config["column_to_attr"],
+            logger=logger,
+            force_parse=False,
+        )
+
+    # Apply hard-coded extensions for specific modules when the extension specifications is not structured
+    # as a single table in the PDF document
+    _apply_hard_coded_extensions(base_model, args.content_definition)
+
+    # Cache the final model (base or combined, with hard-coded extensions)
+    json_store = JSONSpecStore(logger=logger)
+    cache_file_name = f"{getattr(base_model.metadata, 'table_id', 'unknown')}.json"
+    cache_path = f"./cache/model/{cache_file_name}"
+    json_store.save(base_model, cache_path)
+    logger.info(f"Final model saved as JSON to {cache_path}")
+
+    # Print the model
+    printer = SpecPrinter(base_model, logger=logger)
+    printer.print_table(colorize=True)
+    printer.print_tree(attr_names=["elem_name", "elem_tag"], colorize=True)
+
+if __name__ == "__main__":
+    main()

dcmspec/apps/cli/uidvalues.py

@@ -0,0 +1,84 @@
+"""CLI for extracting, caching, and printing DICOM Unique Identifiers (UIDs) from Part 6.
+
+Features:
+- Download and parse DICOM UID Values table from Part 6 of the DICOM standard.
+- Cache the model as a JSON file for future runs and as a structured representation of the standard.
+- Print the resulting UID Values as a table.
+- Supports caching, configuration files, and command-line options for flexible workflows.
+
+Usage:
+    poetry run python -m src.dcmspec.apps.cli.uidvalues [options]
+
+For more details, use the --help option.
+"""
+
+import os
+import argparse
+from dcmspec.config import Config
+
+from dcmspec.spec_factory import SpecFactory
+from dcmspec.spec_printer import SpecPrinter
+
+
+def main():
+    """CLI for parsing, caching, and printing DICOM Unique Identifiers (UIDs) from Part 6.
+
+    This CLI downloads, caches, and prints the list of DICOM UIDs from Part 6 of the DICOM standard.
+
+    The tool parses the UID Values table to extract UID values, names, keywords, types, and additional information.
+    The output can be printed as a table.
+
+    The resulting model is cached as a JSON file. The primary purpose of this cache file is to provide a structured,
+    machine-readable representation of the DICOM UIDs, which can be used for further processing or integration in other
+    tools. As a secondary benefit, the cache file is also used to speed up subsequent runs of the CLI scripts.
+
+    Usage:
+        poetry run python -m src.dcmspec.apps.cli.uidvalues [options]
+
+    Options:
+        --config (str): Path to the configuration file.
+
+    Example:
+        poetry run python -m src.dcmspec.apps.cli.uidvalues
+
+    """
+    # Parse command-line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--config", help="Path to the configuration file")
+    args = parser.parse_args()
+
+    # Determine config file location
+    config_file = args.config or os.getenv("DCMSPEC_CONFIG", None)
+
+    # Initialize configuration
+    config = Config(app_name="dcmspec", config_file=config_file)
+
+    url = "https://dicom.nema.org/medical/dicom/current/output/html/part06.html"
+    cache_file_name = "Part6.xhtml"
+    model_file_name = "UIDValues.json"
+
+    table_id = "table_A-1"
+
+    # Create the factory
+    factory = SpecFactory(
+        column_to_attr={0: "uid_value", 1: "uid_name", 2: "uid_keyword", 3: "uid_type", 4: "uid_part"},
+        name_attr="uid_value",
+        config=config
+    )
+
+    # Download, parse, and cache the model
+    model = factory.create_model(
+        url=url,
+        cache_file_name=cache_file_name,
+        json_file_name=model_file_name,
+        table_id=table_id,
+        force_download=False,
+    )
+
+    # Print the model as a table
+    printer = SpecPrinter(model)
+    printer.print_table(colorize=True)
+
+
+if __name__ == "__main__":
+    main()

dcmspec/apps/cli/upsdimseattributes.py

@@ -0,0 +1,109 @@
+"""CLI for extracting, caching, and printing DICOM UPS DIMSE Service Attribute tables from Part 4.
+
+Features:
+- Download and parse UPS DIMSE Service Attribute table from Part 4 of the DICOM standard.
+- Select a specific DIMSE service and role for filtering.
+- Cache the model as a JSON file for future runs and as a structured representation of the standard.
+- Print the resulting attributes as a table.
+- Supports caching, configuration files, and command-line options for flexible workflows.
+
+Usage:
+    poetry run python -m src.dcmspec.apps.cli.upsdimseattributes [options]
+
+For more details, use the --help option.
+"""
+
+import os
+import argparse
+from dcmspec.config import Config
+
+from dcmspec.service_attribute_model import ServiceAttributeModel
+from dcmspec.spec_factory import SpecFactory
+from dcmspec.spec_printer import SpecPrinter
+from dcmspec.ups_xhtml_doc_handler import UPSXHTMLDocHandler
+from dcmspec.service_attribute_defaults import UPS_DIMSE_MAPPING, UPS_COLUMNS_MAPPING, UPS_NAME_ATTR
+
+
+def main():
+    """CLI for parsing, caching, and printing DICOM UPS DIMSE Service Attribute tables from Part 4.
+
+    This CLI downloads, caches, and prints the attributes for the UPS DIMSE services from Part 4 of the DICOM standard.
+
+    The tool parses the UPS Service Attribute table and allows selection of a specific DIMSE service (e.g., N-CREATE,
+    N-SET, N-GET, C-FIND, FINAL) and role (SCU or SCP). The output can be printed as a table.
+
+    The resulting model is cached as a JSON file. The primary purpose of this cache file is to provide a structured,
+    machine-readable representation of the UPS DIMSE service attributes, which can be used for further processing or
+    integration in other tools. As a secondary benefit, the cache file is also used to speed up subsequent runs of the
+    CLI scripts.
+
+    Usage:
+        poetry run python -m src.dcmspec.apps.cli.upsdimseattributes [options]
+
+    Options:
+        --config (str): Path to the configuration file.
+        --dimse (str): DIMSE service to select (ALL_DIMSE, N-CREATE, N-SET, N-GET, C-FIND, FINAL).
+        --role (str): Role to select (SCU or SCP). Only valid if --dimse is not ALL_DIMSE.
+
+    Example:
+        poetry run python -m src.dcmspec.apps.cli.upsdimseattributes --dimse N-CREATE --role SCU
+
+    """
+    # Parse command-line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--config", help="Path to the configuration file")
+    parser.add_argument(
+        "--dimse",
+        choices=["ALL_DIMSE", "N-CREATE", "N-SET", "N-GET", "C-FIND", "FINAL"],
+        default="ALL_DIMSE",
+        help="DIMSE service to select (default: ALL_DIMSE)",
+    )
+    parser.add_argument(
+        "--role",
+        choices=["SCU", "SCP"],
+        help="Role to select (SCU or SCP)",
+    )
+    args = parser.parse_args()
+
+    # Determine config file location
+    config_file = args.config or os.getenv("DCMSPEC_CONFIG", None)
+    
+    # Initialize configuration
+    config = Config(app_name="dcmspec", config_file=config_file)
+
+    url = "https://dicom.nema.org/medical/dicom/current/output/chtml/part04/sect_CC.2.5.html"
+    cache_file_name = "UPSattributes.xhtml"
+    table_id = "table_CC.2.5-3"  
+    
+    # Create the factory with UPSXHTMLDocHandler for UPS-specific table patching
+    factory = SpecFactory(
+        model_class=ServiceAttributeModel,
+        input_handler=UPSXHTMLDocHandler(config=config),
+        column_to_attr=UPS_COLUMNS_MAPPING,
+        name_attr=UPS_NAME_ATTR,
+        config=config
+    )
+
+    # Download, parse, and cache the model
+    model = factory.create_model(
+        url=url,
+        cache_file_name=cache_file_name,
+        table_id=table_id,
+        force_download=False,
+        model_kwargs={"dimse_mapping": UPS_DIMSE_MAPPING},
+    )
+
+    if args.dimse!= "ALL_DIMSE":
+        model.select_dimse(args.dimse)
+    if args.role:
+        if args.dimse == "ALL_DIMSE":
+            parser.error("--role option can only be used if --dimse is not ALL_DIMSE")
+        model.select_role(args.role)
+
+    # Print the model as a table
+    printer = SpecPrinter(model)
+    printer.print_table(colorize=True)
+
+
+if __name__ == "__main__":
+    main()