Merge pull request #120 from pydicom/add/tag-groups

Adding tag groups for values and fields

Author: vsoch

CHANGELOG.md

@@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
 Referenced versions in headers are tagged on Github, in parentheses are for pypi.
 
 ## [vxx](https://github.com/pydicom/deid/tree/master) (master)
+ - adding support for tag groups (values, fields) (0.1.4)
  - Adding option to provide function to remove (must return boolean) (0.1.38)
  - removing matplotlib version requirement (0.1.37)
  - Matplotlib dependency >= 2.1.2 (0.1.36)

deid/config/__init__.py

@@ -91,28 +91,40 @@ def _get_section(self, name):
         """
         section = None
         if self.deid is not None:
-            if name in self.deid:
-                section = self.deid[name]
+            section = self.deid.get(name)
         return section
 
+    # Get Sections
+
     def get_format(self):
         """return the format of the loaded deid, if one exists
         """
         return self._get_section("format")
 
+    def _get_named_section(self, section_name, name=None):
+        """a helper function to return an entire section, or if a name is
+           provided, a named section under it. If the section is not
+           defined, we appropriately return None.
+        """
+        section = self._get_section(section_name)
+        if name is not None and section is not None:
+            section = section.get(name, [])
+        return section
+
     def get_filters(self, name=None):
         """return all filters for a deid recipe, or a set based on a name
         """
-        filters = self._get_section("filter")
-        if name is not None and filters is not None:
-            filters = filters[name]
-        return filters
+        return self._get_named_section("filter", name)
 
-    def ls_filters(self):
-        """list names of filter groups
+    def get_values_lists(self, name=None):
+        """return a values list by name
         """
-        filters = self._get_section("filter")
-        return list(filters.keys())
+        return self._get_named_section("values", name)
+
+    def get_fields_lists(self, name=None):
+        """return a values list by name
+        """
+        return self._get_named_section("fields", name)
 
     def get_actions(self, action=None, field=None):
         """get deid actions to perform on a header, or a subset based on a type
@@ -137,6 +149,38 @@ def get_actions(self, action=None, field=None):
 
         return header
 
+    # Boolean properties
+
+    def _has_list_content(self, name):
+        return len(self.deid.get(name, [])) > 0
+
+    def has_fields_lists(self):
+        return self._has_list_content("fields")
+
+    def has_values_lists(self):
+        return self._has_list_content("values")
+
+    def has_actions(self):
+        return self._has_list_content("header")
+
+    # Listing
+
+    def listof(self, section):
+        """return a list of keys for a section"""
+        listing = self._get_section(section) or {}
+        return list(listing.keys())
+
+    def ls_filters(self):
+        return self.listof("filter")
+
+    def ls_valuelists(self):
+        return self.listof("values")
+
+    def ls_fieldlists(self):
+        return self.listof("fields")
+
+    # Init
+
     def _init_deid(self, deid=None, base=False, default_base="dicom"):
         """initalize the recipe with one or more deids, optionally including 
            the default. This function is called at init time. If you need to add

deid/config/standards.py

@@ -26,10 +26,15 @@
 formats = ["dicom"]
 
 # Supported Sections
-sections = ["header", "labels", "filter"]
+sections = ["header", "labels", "filter", "values", "fields"]
 
+# Supported Header Actions
 actions = ("ADD", "BLANK", "JITTER", "KEEP", "REPLACE", "REMOVE", "LABEL")
 
+# Supported Group actions (SPLIT only supported for values)
+groups = ["values", "fields"]
+group_actions = ("FIELD", "SPLIT")
+
 # Valid actions for a filter action
 filters = (
     "contains",

deid/config/utils.py

@@ -28,10 +28,16 @@
 # pylint: skip-file
 
 from deid.logger import bot
-from deid.utils import read_file
+from deid.utils import read_file, get_installdir
 from deid.data import data_base
-from deid.config.standards import formats, actions, sections, filters
-
+from deid.config.standards import (
+    formats,
+    actions,
+    sections,
+    filters,
+    groups,
+    group_actions,
+)
 from collections import OrderedDict
 import os
 import re
@@ -130,7 +136,7 @@ def load_deid(path=None):
     config = OrderedDict()
     section = None
 
-    while len(spec) > 0:
+    while spec:
 
         # Clean up white trailing/leading space
         line = spec.pop(0).strip()
@@ -139,15 +145,9 @@ def load_deid(path=None):
         if line.startswith("#"):
             continue
 
-        # Starts with Format?
-        elif bool(re.match("format", line, re.I)):
-            fmt = re.sub("FORMAT|(\s+)", "", line).lower()
-            if fmt not in formats:
-                bot.exit("%s is not a valid format." % fmt)
-
-            # Set format
-            config["format"] = fmt
-            bot.debug("FORMAT set to %s" % fmt)
+        # Set format
+        elif bool(re.match("^format", line, re.I)):
+            config["format"] = parse_format(line)
 
         # A new section?
         elif line.startswith("%"):
@@ -168,24 +168,18 @@ def load_deid(path=None):
                 config=config, section=section, section_name=section_name
             )
 
-        # An action (replace, blank, remove, keep, jitter)
+        # A %fields action (only field allowed), %values allows split
+        elif line.upper().startswith(group_actions) and section in groups:
+            config = parse_group_action(
+                section=section, section_name=section_name, line=line, config=config
+            )
+
+        # An action (ADD, BLANK, JITTER, KEEP, REPLACE, REMOVE, LABEL)
         elif line.upper().startswith(actions):
 
             # Start of a filter group
             if line.upper().startswith("LABEL") and section == "filter":
-                members = []
-                keep_going = True
-                while keep_going is True:
-                    next_line = spec[0]
-                    if next_line.upper().strip().startswith("LABEL"):
-                        keep_going = False
-                    elif next_line.upper().strip().startswith("%"):
-                        keep_going = False
-                    else:
-                        new_member = spec.pop(0)
-                        members.append(new_member)
-                    if len(spec) == 0:
-                        keep_going = False
+                members = parse_filter_group(spec)
 
                 # Add the filter label to the config
                 config = parse_label(
@@ -201,7 +195,7 @@ def load_deid(path=None):
                     section=section, section_name=section_name, line=line, config=config
                 )
         else:
-            bot.debug("%s not recognized to be in valid format, skipping." % line)
+            bot.warning("%s not recognized to be in valid format, skipping." % line)
     return config
 
 
@@ -214,6 +208,9 @@ def find_deid(path=None):
        path: a path on the filesystem. If not provided, will assume PWD.
 
     """
+    # A default deid will be loaded if all else fails
+    default_deid = os.path.join(get_installdir(), "data", "deid.dicom")
+
     if path is None:
         path = os.getcwd()
 
@@ -224,7 +221,11 @@ def find_deid(path=None):
         ]
 
         if len(contenders) == 0:
-            bot.exit("No deid settings files found in %s, exiting." % (path))
+            bot.warning(
+                "No deid settings files found in %s, will use default dicom.deid."
+                % path
+            )
+            contenders.append(default_deid)
 
         elif len(contenders) > 1:
             bot.warning("Multiple deid files found in %s, will use first." % (path))
@@ -238,6 +239,48 @@ def find_deid(path=None):
     return path
 
 
+def parse_format(line):
+    """given a line that starts with FORMAT, parse the format of the
+       file and check that it is supported. If not, exit on error. If yes,
+       return the format.
+
+       Parameters
+       ==========
+       line: the line that starts with format.
+    """
+    fmt = re.sub("FORMAT|(\s+)", "", line).lower()
+    if fmt not in formats:
+        bot.exit("%s is not a valid format." % fmt)
+    bot.debug("FORMAT set to %s" % fmt)
+    return fmt
+
+
+def parse_filter_group(spec):
+    """given the specification (a list of lines) continue parsing lines
+       until the filter group ends, as indicated by the start of a new LABEL,
+       (case 1), the start of a new section (case 2) or the end of the spec
+       file (case 3). Returns a list of members (lines) that belong to the
+       filter group. The list (by way of using pop) is updated in the calling
+       function.
+
+       Parameters
+       ==========
+       spec: unparsed lines of the deid recipe file
+    """
+    members = []
+    keep_going = True
+    while keep_going and spec:
+        next_line = spec[0]
+        if next_line.upper().strip().startswith("LABEL"):
+            keep_going = False
+        elif next_line.upper().strip().startswith("%"):
+            keep_going = False
+        else:
+            new_member = spec.pop(0)
+            members.append(new_member)
+    return members
+
+
 def parse_label(section, config, section_name, members, label=None):
     """parse label will add a (optionally named) label to the filter
        section, including one or more criteria
@@ -289,7 +332,10 @@ def parse_label(section, config, section_name, members, label=None):
 
 
 def parse_member(members, operator=None):
-
+    """a parsing function for a filter member. Will return a single member
+       with fields, values, and an operator. In the case of multiple and/or
+       statements that are chained, will instead return a list.
+    """
     main_operator = operator
 
     actions = []
@@ -382,7 +428,7 @@ def add_section(config, section, section_name=None):
     if section is None:
         bot.exit("You must define a section (e.g. %header) before any action.")
 
-    if section == "filter" and section_name is None:
+    if section in ["filter", "values", "fields"] and section_name is None:
         bot.exit("You must provide a name for a filter section.")
 
     if section not in sections:
@@ -415,6 +461,54 @@ def _remove_comments(parts):
     return value.split("#")[0]  # remove comments
 
 
+def parse_group_action(section, line, config, section_name):
+    """parse a group action, either FIELD or SPLIT, which must belong to
+       either a fields or values section.
+
+       Parameters
+       =========
+       section: a valid section name from the deid config file
+       line: the line content to parse for the section/action
+       config: the growing/current config dictionary
+       section_name: optionally, a section name
+    """
+    if not line.upper().startswith(group_actions):
+        bot.exit("%s is not a valid group action." % line)
+
+    if not line.upper().startswith("FIELD") and section == "fields":
+        bot.exit("%fields only supports FIELD actions.")
+
+    # We may have to deal with cases of spaces
+    bot.debug("%s: adding %s" % (section, line))
+    parts = line.split(" ")
+    action = parts.pop(0).replace(" ", "")
+
+    # Both require some parts
+    if not parts:
+        bot.exit("%s action %s requires additional arguments" % (section, action))
+
+    # For both, the second is always a field or field expander
+    field = parts.pop(0)
+
+    # Fields supports one or more fields with expanders (no third arguments)
+    if section == "fields":
+        config[section][section_name].append({"action": action, "field": field})
+
+    # Values supports FIELD or SPLIT
+    elif section == "values":
+
+        # If we have a third set of arguments
+        if parts:
+            value = _remove_comments(parts)
+            config[section][section_name].append(
+                {"action": action, "field": field, "value": value}
+            )
+        else:
+            config[section][section_name].append({"action": action, "field": field})
+
+    return config
+
+
 def parse_config_action(section, line, config, section_name=None):
     """add action will take a line from a deid config file, a config (dictionary), and
        an active section name (eg header) and add an entry to the config file to perform
@@ -428,7 +522,6 @@ def parse_config_action(section, line, config, section_name=None):
        section_name: optionally, a section name
 
     """
-
     if not line.upper().startswith(actions):
         bot.exit("%s is not a valid action line." % line)
 

deid/dicom/__init__.py

@@ -6,7 +6,5 @@
 )
 
 from .utils import get_files
-
 from .fields import extract_sequence
-
 from .pixels import has_burned_pixels, DicomCleaner