keep_masked_pixels is read from config

py/picca/delta_extraction/config.py

@@ -163,7 +163,6 @@ def __init__(self, filename):
         self.__format_corrections_section()
         self.masks = None
         self.num_masks = None
-        self.keep_masked_pixels = False
         self.__format_masks_section()
         self.data = None
         self.__format_data_section()
@@ -504,8 +503,6 @@ def __format_masks_section(self):
             raise ConfigError("In section [masks], variable 'num masks' "
                               "must be a non-negative integer")
 
-        self.keep_masked_pixels = section.getboolean("keep pixels", fallback=False)
-
         # check that arguments are valid
         for key in section.keys():
             if key not in accepted_masks_options:

py/picca/delta_extraction/mask.py

@@ -20,8 +20,8 @@ class Mask:
 
     Arguments
     ---------
-    keep_masked_pixels: bool (default: False)
-    Determines the method to mask pixels. If true, sets ivar to 0.
+    config: configparser.SectionProxy
+    Parsed options to initialize class
 
     Methods
     -------
@@ -37,9 +37,11 @@ class Mask:
     If keep_masked_pixels=True, then points to _set_ivar_to_zero.
     Otherwise, points to _remove_pixels.
     """
-    def __init__(self, keep_masked_pixels=False):
+    def __init__(self, config):
         """Initialize class instance"""
         self.los_id = {}
+
+        keep_masked_pixels = config.getboolean("keep pixels", fallback=False)
 
         if keep_masked_pixels:
             self._masker = _set_ivar_to_zero

py/picca/delta_extraction/masks/absorber_mask.py

@@ -35,7 +35,7 @@ class AbsorberMask(Mask):
     logger: logging.Logger
     Logger object
     """
-    def __init__(self, config, keep_masked_pixels=False):
+    def __init__(self, config):
         """Initialize class instance.
 
         Arguments
@@ -45,7 +45,7 @@ def __init__(self, config, keep_masked_pixels=False):
         """
         self.logger = logging.getLogger(__name__)
 
-        super().__init__(keep_masked_pixels)
+        super().__init__(config)
 
         # first load the absorbers catalogue
         filename = config.get("filename")

py/picca/delta_extraction/masks/bal_mask.py

@@ -62,17 +62,14 @@ class BalMask(Mask):
     logger: logging.Logger
     Logger object
     """
-    def __init__(self, config, keep_masked_pixels=False):
+    def __init__(self, config):
         """Initializes class instance.
 
         Arguments
         ---------
         config: configparser.SectionProxy
         Parsed options to initialize class
 
-        keep_masked_pixels: bool (default: False)
-        Determines the method to mask pixels. If true, sets ivar to 0.
-
         Raise
         -----
         MaskError if there are missing variables
@@ -82,7 +79,7 @@ def __init__(self, config, keep_masked_pixels=False):
         """
         self.logger = logging.getLogger(__name__)
 
-        super().__init__(keep_masked_pixels)
+        super().__init__(config)
 
         filename = config.get("filename")
         if filename is None:
@@ -237,4 +234,4 @@ def apply_mask(self, forest):
 
         # do the actual masking
         for param in Forest.mask_fields:
-                self._masker(forest, param, w)
+            self._masker(forest, param, w)

py/picca/delta_extraction/masks/dla_mask.py

@@ -45,17 +45,14 @@ class DlaMask(Mask):
     mask: astropy.Table
     Table containing specific intervals of wavelength to be masked for DLAs
     """
-    def __init__(self, config, keep_masked_pixels=False):
+    def __init__(self, config):
         """Initializes class instance.
 
         Arguments
         ---------
         config: configparser.SectionProxy
         Parsed options to initialize class
 
-        keep_masked_pixels: bool (default: False)
-        Determines the method to mask pixels. If true, sets ivar to 0.
-
         Raise
         -----
         MaskError if there are missing variables
@@ -66,7 +63,7 @@ def __init__(self, config, keep_masked_pixels=False):
         """
         self.logger = logging.getLogger(__name__)
 
-        super().__init__(keep_masked_pixels)
+        super().__init__(config)
 
         # first load the dla catalogue
         filename = config.get("filename")

py/picca/delta_extraction/masks/lines_mask.py

@@ -32,15 +32,15 @@ class LinesMask(Mask):
     Table with the observed-frame wavelength of the lines to mask. This usually
     contains the sky lines.
     """
-    def __init__(self, config, keep_masked_pixels=False):
+    def __init__(self, config):
         """Initialize class instance.
 
         Arguments
         ---------
         config: configparser.SectionProxy
         Parsed options to initialize class
         """
-        super().__init__(keep_masked_pixels)
+        super().__init__(config)
 
         mask_file = config.get("filename")
         if mask_file is None:

py/picca/delta_extraction/survey.py

@@ -248,7 +248,7 @@ def read_masks(self):
         self.logger.info(f"Reading masks. There are {num_masks} masks")
 
         for MaskType, mask_arguments in self.config.masks:
-            mask = MaskType(mask_arguments, self.config.keep_masked_pixels)
+            mask = MaskType(mask_arguments)
             self.masks.append(mask)
 
         t1 = time.time()

py/picca/tests/delta_extraction/mask_tests.py

@@ -180,7 +180,9 @@ def test_mask(self):
 
         Load a Mask instace and check that method apply_mask is not initialized.
         """
-        mask = Mask()
+        config = ConfigParser()
+        config.read_dict({"masks": {}})
+        mask = Mask(config['masks'])
         expected_message = (
             "Function 'apply_mask' was not overloaded by child class")
         with self.assertRaises(MaskError) as context_manager: