metis_cal_chophome skeleton

metisp/pymetis/src/pymetis/inputs/common.py

@@ -30,7 +30,7 @@
 
  -  `SinglePipelineInput` (for `Input` classes with a single Frame)
  -  `MultiplePipelineInput` (for `Input` classes with a FrameSet)
- 
+
 You should override class attributes:
 
  -  `_title`
@@ -101,3 +101,7 @@ class WavecalInput(SinglePipelineInput):
     _group: cpl.ui.Frame.FrameGroup = cpl.ui.Frame.FrameGroup.CALIB
 
 
+class PinholeTableInput(SinglePipelineInput):
+    _title: str = "pinhole table"
+    _tags: Pattern = re.compile(r"WCU_PINHOLE_TABLE")
+    _group: cpl.ui.Frame.FrameGroup = cpl.ui.Frame.FrameGroup.CALIB

metisp/pymetis/src/pymetis/recipes/cal/metis_cal_chophome.py

@@ -0,0 +1,184 @@
+"""
+This file is part of the METIS Pipeline.
+Copyright (C) 2024 European Southern Observatory
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+"""
+
+import re
+from typing import Dict
+
+import cpl
+from cpl.core import Msg
+
+from pymetis.base.recipe import MetisRecipe
+from pymetis.inputs import RawInput
+from pymetis.inputs.common import (LinearityInput, GainMapInput,
+                                   PersistenceMapInput, BadpixMapInput,
+                                   PinholeTableInput)
+from pymetis.base.product import PipelineProduct
+from pymetis.prefab.rawimage import RawImageProcessor
+
+class MetisCalChophomeImpl(RawImageProcessor):  # TODO replace parent class?
+    """Implementation class for metis_cal_chophome"""
+    target = "LM_CHOPHOME"
+
+    class InputSet(RawImageProcessor.InputSet):
+        """Inputs for metis_cal_chophome"""
+        class RawInput(RawInput):
+            _tags = re.compile(r"LM_CHOPHOME_RAW")
+
+        class DarkInput(RawInput):
+            _tags = re.compile(r"LM_WCU_OFF_RAW")
+
+        def __init__(self, frameset: cpl.ui.FrameSet):
+            super().__init__(frameset)
+            self.raw = self.RawInput(frameset)
+            self.background = self.DarkInput(frameset)
+            self.linearity = LinearityInput(frameset)
+            self.gain_map = GainMapInput(frameset)
+            self.persistence = PersistenceMapInput(frameset, required=False)
+            self.badpixmap = BadpixMapInput(frameset, required=False)
+            self.pinhole_table = PinholeTableInput(frameset, required=True)
+
+            self.inputs += [self.raw, self.background, self.linearity, self.gain_map,
+                            self.badpixmap, self.persistence]
+
+
+    class ProductCombined(PipelineProduct):
+        """
+        Final product: combined, background-subtracted images of the WCU source
+        """
+        group = cpl.ui.Frame.FrameGroup.PRODUCT
+        level = cpl.ui.Frame.FrameLevel.FINAL
+        frame_type = cpl.ui.Frame.FrameType.IMAGE
+
+        @property
+        def category(self) -> str:
+            return "LM_CHOPHOME_COMBINED"
+
+        @property
+        def output_file_name(self) -> str:
+            return f"{self.category}.fits"
+
+        @property
+        def tag(self) -> str:
+            return rf"{self.category}"
+
+
+    class ProductBackground(PipelineProduct):
+        """
+        Intermediate product: the instrumental background (WCU OFF)
+        """
+        group = cpl.ui.Frame.FrameGroup.PRODUCT
+        level = cpl.ui.Frame.FrameLevel.INTERMEDIATE
+        frame_type = cpl.ui.Frame.FrameType.IMAGE
+
+        @property
+        def category(self) -> str:
+            return "LM_CHOPHOME_BACKGROUND"
+
+        @property
+        def output_file_name(self) -> str:
+            return f"{self.category}.fits"
+
+        @property
+        def tag(self) -> str:
+            return rf"{self.category}"
+
+
+    def process_images(self) -> Dict[str, PipelineProduct]:
+        """do something"""
+
+        background_hdr = cpl.core.PropertyList()
+        self.inputset.background.frameset.dump()
+        bg_images = self.load_images(self.inputset.background.frameset)
+        background_img = self.combine_images(bg_images, "median")
+        # TODO: define usedframes
+
+        combined_hdr = cpl.core.PropertyList()
+        raw_images = self.load_images(self.inputset.raw.frameset)
+        raw_images.subtract_image(background_img)
+        combined_img = self.combine_images(raw_images, "median")
+
+        self.products = {
+            rf"{self.target}_COMBINED":
+            self.ProductCombined(self, combined_hdr, combined_img),
+            rf"{self.target}_BACKGROUND":
+            self.ProductBackground(self, background_hdr, background_img),
+        }
+        return self.products
+
+    def load_images(self, frameset: cpl.ui.FrameSet) -> cpl.core.ImageList:
+        """Load an imagelist from a FrameSet
+
+        This is a temporary implementation that should be generalised to the
+        entire pipeline package. It uses cpl functions - these should be
+        replaced with hdrl functions once they become available, in order
+        to use uncertainties and masks.
+        """
+        output = cpl.core.ImageList()
+
+        for idx, frame in enumerate(frameset):
+            Msg.info(self.__class__.__qualname__,
+                     f"Processing input frame #{idx}: {frame.file!r}...")
+            output.append(cpl.core.Image.load(frame.file, extension=1))
+
+        return output
+
+
+class MetisCalChophome(MetisRecipe):
+    """Determine chopper home position
+    """
+    # Recipe information
+    _name = "metis_cal_chophome"
+    _version = "0.1"
+    _author = "Oliver Czoske, A*"
+    _email = "[email protected]"
+    _copyright = "GPL-3.0-or-later"
+    _synopsis = "Determination of chopper home position"
+    _description = """\
+    Determine the chopper home position from LM-imaging of the WCU pinhole mask.
+
+        Inputs
+            LM_CHOPHOME_RAW: Raw LM band images [1-n]
+            LM_WCU_RAW_OFF:  Background images with WCU black-body closed [1-n]
+            GAIN_MAP_2RG:    Gain map for 2RG detector
+            LINEARITY_2RG:   Linearity map for 2RG detector
+            BADPIX_MAP_2RG:  Bad-pixel map for 2RG detector [optional]
+            PINHOLE_TABLE:   Table with location of pinhole on mask
+            PERSISTENCE_MAP: Persistence map [optional]
+
+        Outputs
+            LM_CHOPHOME_BACKGROUND: Average of background images (WCU_OFF)
+            LM_CHOPHOME_COMBINED: Stacked background-subtracted images of pinhole mask
+                                  The chopper offset is in the header.
+
+        Algorithm
+           The position of the pinhole image on the detector is measured from the stacked
+           background-subtracted images. The measured position is compared to the WFS
+           metrology to give the chopper home position.
+    """
+
+    parameters = cpl.ui.ParameterList([
+        cpl.ui.ParameterEnum(
+            name="metis_cal_chophome.stacking.method",
+            context="metis_cal_chophome",
+            description="Name of the method used to combine the input images",
+            default="average",
+            alternatives=("add", "average", "median", "sigclip"),
+        ),
+])     # no parameters defined in DRLD
+    implementation_class = MetisCalChophomeImpl

metisp/pymetis/src/pymetis/tests/conftest.py

@@ -47,7 +47,7 @@ def inner(filename: str):
         frameset = cpl.ui.FrameSet()
         with open(root / filename) as f:
             for line in f.readlines():
-                tokens = line.rstrip('\n').split(' ')
+                tokens = line.rstrip('\n').split()
                 path = os.path.expandvars(tokens[0])
                 frameset.append(cpl.ui.Frame(path, tag=tokens[1]))
 

metisp/pymetis/src/pymetis/tests/test_metis_cal_chophome.py

@@ -0,0 +1,51 @@
+"""
+This file is part of the METIS Pipeline.
+Copyright (C) 2024 European Southern Observatory
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+"""
+
+import pytest
+
+from pymetis.recipes.cal.metis_cal_chophome import (MetisCalChophome as Recipe,
+                                                    MetisCalChophomeImpl as Impl)
+from generic import BaseInputSetTest, BaseRecipeTest, BaseProductTest
+
+
+@pytest.fixture
+def name():
+    return 'metis_cal_chophome'
+
+
+@pytest.fixture
+def sof(name):
+    return f"{name}.sof"
+
+
+class TestRecipe(BaseRecipeTest):
+    """ A bunch of extremely simple test cases... just to see if it does something """
+    _recipe = Recipe
+
+
+class TestInputSet(BaseInputSetTest):
+    impl = Impl
+    count = 3
+
+
+class TestProductCombined(BaseProductTest):
+    product = Impl.ProductCombined
+
+class TestProductBackground(BaseProductTest):
+    product = Impl.ProductBackground

metisp/pyrecipes/metis_recipes.py

@@ -27,6 +27,7 @@
 from pymetis.recipes.ifu.metis_ifu_postprocess import MetisIfuPostprocess
 from pymetis.recipes.ifu.metis_ifu_reduce import MetisIfuReduce
 from pymetis.recipes.ifu.metis_ifu_telluric import MetisIfuTelluric
+from pymetis.recipes.cal.metis_cal_chophome import MetisCalChophome
 
 __all__ = [
     MetisDetLinGain,
@@ -39,5 +40,5 @@
     MetisIfuPostprocess,
     MetisIfuReduce,
     MetisIfuTelluric,
+    MetisCalChophome,
 ]
-