Merge branch 'feature-multiple-mask-files' into development

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/)
 ### Added
  - Process Plugin support for List Data
  - Adds Exception handling to Processes
+ - PyMask support for multiple masking files.
 ### Changed
  - Removed previous_event from Process Interface
  - Duplex Pipes are used over Simplex Pipes for Duplex Processes

PyPWA/progs/masking/__init__.py

@@ -50,7 +50,7 @@ def __add_input_argument(self):
 
     def __add_masking_argument(self):
         self._parser.add_argument(
-            "--mask", "-m", type=str,help="Masking file"
+            "--mask", "-m", type=str, action="append", help="Masking file"
         )
 
     def __add_output_file(self):

PyPWA/progs/masking/masking.py

@@ -25,6 +25,7 @@
 
 import logging
 import warnings
+from typing import List
 from typing import Optional as Opt
 
 import numpy
@@ -60,7 +61,7 @@ def __setup_data(self, input_file, output_file, masking_file, parser):
         # type: (str, str, Opt[str], plugins.DataParser) -> None
         self.__load_writer(input_file, output_file)
         self.__load_reader(input_file)
-        self.__setup_masking_file(masking_file, parser)
+        self.__setup_mask_array(masking_file, parser)
 
     def __load_writer(self, input_file, output_file):
         # type: (str, str) -> None
@@ -73,13 +74,23 @@ def __load_reader(self, input_file):
         # type: (str) -> None
         self.__reader = self.__iterator.return_reader(input_file)
 
-    def __setup_masking_file(self, masking_file, parser):
-        # type: (Opt[str],  plugins.DataParser) -> None
+    def __setup_mask_array(self, masking_file, parser):
+        # type: (Opt[List[str]],  plugins.DataParser) -> None
         if masking_file:
-            self.__mask = parser.parse(masking_file)
+            self.__mask = self.__load_masking_files(masking_file, parser)
         else:
             self.__mask = numpy.ones(len(self.__reader), dtype=bool)
 
+    def __load_masking_files(self, masking_files, parser):
+        # type: (List[str],  plugins.DataParser) -> numpy.ndarray
+        mask = None  # type: numpy.ndarray
+        for file in masking_files:
+            if isinstance(mask, type(None)):
+                mask = parser.parse(file)
+            else:
+                mask += parser.parse(file)
+        return mask
+
     @property
     def reader(self):
         # type: () -> internals.Reader

tests/data/test_docs/sv_test_data2.pf

@@ -0,0 +1,4 @@
+0
+0
+1
+0

tests/progs/masking/test_masking.py

@@ -4,6 +4,7 @@
 import pytest
 
 from PyPWA.entries import arguments
+from PyPWA.core.shared import file_libs
 
 """
 Masking Data
@@ -17,6 +18,10 @@
     os.path.dirname(__file__), "../../data/test_docs/sv_test_data.pf"
 )
 
+PF2 = os.path.join(
+    os.path.dirname(__file__), "../../data/test_docs/sv_test_data2.pf"
+)
+
 PF_SHORT = os.path.join(
     os.path.dirname(__file__), "../../data/test_docs/sv_test_data_short.pf"
 )
@@ -25,11 +30,11 @@
     os.path.dirname(__file__), "../../data/test_docs/sv_test_data_long.pf"
 )
 
+
 """
 Test Masking with Standard Data
 """
 
-
 @pytest.fixture()
 def correct_argv(monkeypatch):
     original = sys.argv
@@ -45,7 +50,7 @@ def cleanup_temp():
 
 tested_args = [
     ["pymask", "--input", INPUT, "-o", "testfile.txt"],
-    ["pymask", "-i", INPUT, "--mask", PF, "-o", "testfile.txt"]
+    ["pymask", "-i", INPUT, "--mask", PF, "-m", PF2, "-o", "testfile.txt"]
 ]
 @pytest.fixture(params=tested_args)
 def patch_args_clean(monkeypatch, request, correct_argv, cleanup_temp):
@@ -57,9 +62,29 @@ def test_masking_utility(patch_args_clean):
 
 
 """
-Test Masking with more masked events than data
+Test Masking with Standard Data
 """
 
+@pytest.fixture()
+def patch_args_double_mask(monkeypatch, request, correct_argv, cleanup_temp):
+    monkeypatch.setattr(
+        "sys.argv",
+        [
+            "pymask",
+            "-i", INPUT, "--mask", PF, "-m", PF2, "-o", "testfile.txt"
+        ]
+    )
+    arguments.masking_utility()
+    yield
+
+
+def test_masking_utility_has_correct_number_of_lines(patch_args_double_mask):
+    assert file_libs.get_file_length("testfile.txt") == 1
+
+
+"""
+Test Masking with more masked events than data
+"""
 
 @pytest.fixture()
 def patch_args_warning(monkeypatch, correct_argv, cleanup_temp):
@@ -78,7 +103,6 @@ def test_masking_warning(patch_args_warning):
 Test Masking with less masked events than data
 """
 
-
 @pytest.fixture()
 def patch_args_critical(monkeypatch, correct_argv, cleanup_temp):
     monkeypatch.setattr(