adding stop_before_pixels to read_file of dicom parser

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 stop_before_pixels to read_file in parser (0.2.24)
  - removing verbosity of debug logger (0.2.23)
  - changing iteration technique through fields to properly add nested uids [#153](https://github.com/pydicom/deid/issues/153) (0.2.22)
  - change to return results from detect when recipe does not contain filters [#155](https://github.com/pydicom/deid/issues/155)

deid/dicom/header.py

@@ -44,7 +44,12 @@
 
 
 def get_identifiers(
-    dicom_files, force=True, config=None, strip_sequences=False, remove_private=False
+    dicom_files,
+    force=True,
+    config=None,
+    strip_sequences=False,
+    remove_private=False,
+    stop_before_pixels=False,
 ):
     """extract all identifiers from a dicom image.
     This function returns a lookup by file name, where each value indexed

deid/dicom/parser.py

@@ -53,7 +53,9 @@ class DicomParser:
     file. For each, we store the element and child elements
     """
 
-    def __init__(self, dicom_file, recipe=None, config=None, force=True):
+    def __init__(
+        self, dicom_file, recipe=None, config=None, force=True, stop_before_pixels=False
+    ):
 
         # Lookup for the dicom
         self.lookup = {}
@@ -70,7 +72,7 @@ def __init__(self, dicom_file, recipe=None, config=None, force=True):
         # Deid can be a recipe or filename
         if not isinstance(recipe, DeidRecipe):
             recipe = DeidRecipe(recipe)
-        self.load(dicom_file, force=force)
+        self.load(dicom_file, force=force, stop_before_pixels=stop_before_pixels)
         self.recipe = recipe
 
     def __str__(self):
@@ -79,7 +81,7 @@ def __str__(self):
     def __repr__(self):
         return self.__str__()
 
-    def load(self, dicom_file, force=True):
+    def load(self, dicom_file, force=True, stop_before_pixels=False):
         """Ensure that the dicom file exists, and use full path. Here
         we load the file, and save the dicom, dicom_file, and dicom_name.
         """
@@ -94,7 +96,9 @@ def load(self, dicom_file, force=True):
             # If we must read the file, the path must exist
             if not os.path.exists(dicom_file):
                 bot.exit("%s does not exist." % dicom_file)
-            self.dicom = read_file(dicom_file, force=force)
+            self.dicom = read_file(
+                dicom_file, force=force, stop_before_pixels=stop_before_pixels
+            )
 
         # Set class variables that might be helpful later
         self.dicom_file = os.path.abspath(self.dicom.filename)

deid/version.py

@@ -22,7 +22,7 @@
 
 """
 
-__version__ = "0.2.23"
+__version__ = "0.2.24"
 AUTHOR = "Vanessa Sochat"
 AUTHOR_EMAIL = "[email protected]"
 NAME = "deid"