Add persistence recipe

.github/workflows/run_edps.yaml

@@ -30,6 +30,9 @@ jobs:
       - name: Fetch test data
         run: |
           git clone https://github.com/AstarVienna/METIS_Pipeline_Test_Data.git
+          # Try to checkout a branch in METIS_Pipeline_Test_Data that has
+          # the same name as the branch in METIS_Pipeline that we are testing.
+          git -C METIS_Pipeline_Test_Data checkout "${GITHUB_HEAD_REF}" || true
       - name: Run pytest tests
         run: |
           set +x

metisp/pymetis/src/pymetis/recipes/metis_det_persistence.py

@@ -0,0 +1,145 @@
+"""
+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
+
+from astropy.io import fits
+import cpl
+from cpl.core import Msg
+
+from pymetis.base import MetisRecipeImpl
+from pymetis.base.recipe import MetisRecipe
+from pymetis.base.product import PipelineProduct
+from pymetis.inputs import SinglePipelineInput, PipelineInputSet, RawInput
+
+
+class PersistenceMainInput(SinglePipelineInput):
+    _title: str = "primary raw input"
+    _tags: re.Pattern = re.compile(r"RAW")
+    _group: cpl.ui.Frame.FrameGroup = cpl.ui.Frame.FrameGroup.RAW
+
+
+class MetisDetPersistenceImpl(MetisRecipeImpl):
+
+    class InputSet(PipelineInputSet):
+        """Input to metis_det_persistence
+
+        For now just a single raw image.
+        """
+
+        def __init__(self, frameset: cpl.ui.FrameSet):
+            super().__init__(frameset)
+            self.raw = PersistenceMainInput(frameset)
+            self.others = PersistenceOtherInput(frameset)
+            self.inputs |= {self.raw, self.others}
+
+    class Product(PipelineProduct):
+        """A Persistence Map."""
+        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 r"PERSISTENCE_MAP"
+
+        @property
+        def output_file_name(self) -> str:
+            return fr"{self.category}.fits"
+
+        @property
+        def tag(self) -> str:
+            return self.category
+
+    inputset: InputSet = None
+
+    def process_images(self) -> Dict[str, PipelineProduct]:
+        """
+        This is where the magic happens: all business logic of the recipe should be contained within this function.
+        You can define extra private functions, or use functions from the parent classes:
+        for instance combine_images is a helper function that takes a frameset and a method and returns
+        a single combined frame that is used throughout the pipeline.
+        """
+
+        Msg.info(self.__class__.__qualname__, f"Starting processing image attribute.")
+
+        hdus_raw = fits.open(self.inputset.raw.frame.file)
+        hduss_others = [
+            fits.open(frame.file)
+            for frame in self.inputset.others.frameset
+        ]
+        assert set(len(hdus) for hdus in hduss_others) == {len(hdus_raw)}
+        header_primary_raw = hdus_raw[0].header
+        headers_primary_others = [
+            hdus[0].header for hdus in hduss_others
+        ]
+        assert header_primary_raw["INSTRUME"] == "METIS"
+        assert all(
+            header["INSTRUME"] == "METIS"
+            for header in headers_primary_others
+        )
+        # TODO: Assert all input is from the same subinstrument.
+        # There currently does not seem to be an easy way to determine the
+        # subinstrument from the headers.
+
+        raw = cpl.core.Image.load(self.inputset.raw.frame.file, extension=1)
+
+        persistence = cpl.core.Image.zeros_like(raw)
+        header_primary = cpl.core.PropertyList.load(self.inputset.raw.frame.file, 0)
+
+        self.products = {
+            "PERSISTENCE_MAP": self.Product(self, header_primary, persistence),
+        }
+
+        return self.products
+
+
+class MetisDetPersistence(MetisRecipe):
+    """metis_det_persistence
+
+    metis_det_persistence is usually run by ESO, since it needs all previous
+    observations of the preceding X hours. However, it can also be run by
+    individuals.
+    """
+    # Fill in recipe information
+    _name = "metis_det_persistence"
+    _version = "0.1"
+    _author = "A*"
+    _email = "[email protected]"
+    _copyright = "GPL-3.0-or-later"
+    _synopsis = "Calculates persistence for a single frame"
+    _description = """Calculate persistence."""
+
+    parameters = cpl.ui.ParameterList([
+        cpl.ui.ParameterEnum(
+            name="metis_det_persistence.dummy",
+            context="metis_det_persistence",
+            description="dummy parameter to prevent pyesorex problems",
+            default="1",
+            alternatives=("0", "1"),
+        )
+    ])
+    implementation_class = MetisDetPersistenceImpl
+
+
+class PersistenceOtherInput(RawInput):
+    _title: str = "other raw input"
+    _tags: re.Pattern = re.compile(r"OTHER")
+    _group: cpl.ui.Frame.FrameGroup = cpl.ui.Frame.FrameGroup.CALIB

metisp/pymetis/src/pymetis/tests/test_metis_det_persistence.py

@@ -0,0 +1,45 @@
+"""
+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
+
+import cpl
+
+from pymetis.recipes.metis_det_persistence import MetisDetPersistence as Recipe, MetisDetPersistenceImpl as Impl
+
+from generic import BaseRecipeTest, BaseProductTest, RawInputSetTest
+
+
+@pytest.fixture
+def name():
+    return 'metis_det_persistence'
+
+
+@pytest.fixture
+def sof():
+    return f"metis_det_persistence.sof"
+
+
+class TestRecipe(BaseRecipeTest):
+    """ A bunch of simple and stupid test cases... just to see if it does something """
+    _recipe = Recipe
+
+
+class TestProduct(BaseProductTest):
+    product = Impl.Product

metisp/pyrecipes/metis_recipes.py

@@ -19,6 +19,7 @@
 
 from pymetis.recipes.metis_det_lingain import MetisDetLinGain
 from pymetis.recipes.metis_det_dark import MetisDetDark
+from pymetis.recipes.metis_det_persistence import MetisDetPersistence
 from pymetis.recipes.img.metis_lm_img_basic_reduce import MetisLmImgBasicReduce
 from pymetis.recipes.img.metis_lm_img_flat import MetisLmImgFlat
 from pymetis.recipes.img.metis_lm_img_background import MetisLmImgBackground
@@ -41,6 +42,7 @@
 __all__ = [
     MetisDetLinGain,
     MetisDetDark,
+    MetisDetPersistence,
     MetisLmImgBasicReduce,
     MetisLmImgBackground,
     MetisLmImgStdProcess,