Merge pull request #143 from cta-observatory/move_get_image

Define API for reader and image_mapper

Author: TjarkMiener

.github/workflows/python-package-conda.yml

@@ -29,6 +29,8 @@ jobs:
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
+    - name: Add MKL_THREADING_LAYER variable
+      run:  echo "MKL_THREADING_LAYER=GNU" >> $GITHUB_ENV
     - name: Install dependencies
       run: |
         conda env update --file environment.yml --name base --solver=classic

.zenodo.json

@@ -1,11 +1,6 @@
 {
     "license": "MIT", 
     "contributors": [
-        {
-            "affiliation": "Laboratoire d'Annecy de Physique des Particules, CNRS, and LISTIC,Universit\u00e9 Savoie Mont-Blanc, Annecy, France", 
-            "type": "Researcher", 
-            "name": "Mika\u00ebl Jacquemont"
-        }, 
         {
             "orcid": "0000-0002-5686-2078", 
             "affiliation": "Laboratoire d'Annecy de Physique des Particules, CNRS, Universit\u00e9 Savoie Mont-Blanc, Annecy, France", 
@@ -17,6 +12,12 @@
             "affiliation": "Instituto de F\u00edsica de Part\u00edculas y del Cosmos and Departamento de EMFTEL, Universidad Complutense de Madrid, Madrid, Spain", 
             "type": "Researcher", 
             "name": "Jos\u00e9 Luis Contreras"
+        },
+        {
+            "orcid": "0009-0007-1566-9507", 
+            "affiliation": "Instituto de F\u00edsica de Part\u00edculas y del Cosmos and Departamento de EMFTEL, Universidad Complutense de Madrid, Madrid, Spain", 
+            "type": "Researcher", 
+            "name": "Alexander Cervi\u00f1o"
         }
     ], 
     "language": "eng", 
@@ -30,27 +31,28 @@
     ], 
      "creators": [
         {
-            "affiliation": "University of California Los Angeles, Division of Astronomy and Astrophysics, Los Angeles, CA, USA", 
-            "name": "Bryan Kim"
-        }, 
-        {
-            "affiliation": "Columbia University, Department of Physics, New York, NY, USA", 
-            "name": "Ari Brill"
-        }, 
-        {
-            "affiliation": "Instituto de F\u00edsica de Part\u00edculas y del Cosmos and Departamento de EMFTEL, Universidad Complutense de Madrid, Madrid, Spain", 
+            "orcid": "0000-0003-1821-7964"
+            "affiliation": "Universit\u00e9 de Gen\u00e8ve, D\u00e9partement de physique nucl\u00e9aire et corpusculaire, Gen\u00e8ve, Suisse", 
             "name": "Tjark Miener"
         }, 
         {
             "orcid": "0000-0003-3343-0755", 
             "affiliation": "Instituto de F\u00edsica de Part\u00edculas y del Cosmos and Departamento de EMFTEL, Universidad Complutense de Madrid, Madrid, Spain", 
             "name": "Daniel Nieto"
         }, 
+        {
+            "affiliation": "University of California Los Angeles, Division of Astronomy and Astrophysics, Los Angeles, CA, USA", 
+            "name": "Bryan Kim"
+        }, 
+        {
+            "affiliation": "Columbia University, Department of Physics, New York, NY, USA", 
+            "name": "Ari Brill"
+        }, 
         {
             "affiliation": "Columbia University, Department of Physics, New York, NY, USA", 
             "name": "Qi Feng"
         }
     ], 
     "access_right": "open", 
     "description": "<p>A package of utilities for writing, reading, and applying image processing to&nbsp;calibrated data from imaging atmospheric Cherenkov telescopes in a standardized format.</p>"
-}
+}

README.rst

@@ -43,7 +43,7 @@ necessary package channels, and install dl1-data-handler specified version and i
 
 .. code-block:: bash
 
-   DL1DH_VER=0.12.0
+   DL1DH_VER=0.13.0
    wget https://raw.githubusercontent.com/cta-observatory/dl1-data-handler/v$DL1DH_VER/environment.yml
    conda env create -n [ENVIRONMENT_NAME] -f environment.yml
    conda activate [ENVIRONMENT_NAME]
@@ -52,27 +52,6 @@ necessary package channels, and install dl1-data-handler specified version and i
 This should automatically install all dependencies (NOTE: this may take some time, as by default MKL is included as a dependency of NumPy and it is very large).
 
 
-Dependencies
-------------
-
-The main dependencies are:
-
-
-* PyTables >= 3.8
-* NumPy >= 1.20.0
-* ctapipe == 0.21.2
-
-Also see setup.py.
-
-Usage
------
-
-ImageMapper
-^^^^^^^^^^^
-
-The ImageMapper class transforms the hexagonal input pixels into a 2D Cartesian output image. The basic usage is demonstrated in the `ImageMapper tutorial <https://github.com/cta-observatory/dl1-data-handler/blob/master/notebooks/test_image_mapper.ipynb>`_. It requires `ctapipe-extra <https://github.com/cta-observatory/ctapipe-extra>`_ outside of the dl1-data-handler. See this publication for a detailed description: `arXiv:1912.09898 <https://arxiv.org/abs/1912.09898>`_
-
-
 Links
 -----
 

dl1_data_handler/__init__.py

@@ -1,5 +1,3 @@
 from .image_mapper import *
-from .processor import *
 from .reader import *
-from .transforms import *
 from ._version import __version__

dl1_data_handler/conftest.py

@@ -0,0 +1,59 @@
+"""
+common pytest fixtures for tests in dl1-data-handler.
+Credits to ctapipe for the original code.
+"""
+
+import pytest
+
+from ctapipe.core import run_tool
+from ctapipe.utils import get_dataset_path
+
+@pytest.fixture(scope="session")
+def prod5_gamma_simtel_path():
+    return get_dataset_path("gamma_prod5.simtel.zst")
+
+@pytest.fixture(scope="session")
+def dl1_tmp_path(tmp_path_factory):
+    """Temporary directory for global dl1 test data"""
+    return tmp_path_factory.mktemp("dl1_")
+
+@pytest.fixture(scope="session")
+def r1_tmp_path(tmp_path_factory):
+    """Temporary directory for global r1 test data"""
+    return tmp_path_factory.mktemp("r1_")
+
+@pytest.fixture(scope="session")
+def dl1_gamma_file(dl1_tmp_path, prod5_gamma_simtel_path):
+    """
+    DL1 file containing both images and parameters from a gamma simulation set.
+    """
+    from ctapipe.tools.process import ProcessorTool
+
+    output = dl1_tmp_path / "gamma.dl1.h5"
+
+    argv = [
+        f"--input={prod5_gamma_simtel_path}",
+        f"--output={output}",
+        "--write-images",
+        "--DataWriter.Contact.name=αℓℓ the äüöß",
+    ]
+    assert run_tool(ProcessorTool(), argv=argv, cwd=dl1_tmp_path) == 0
+    return output
+
+@pytest.fixture(scope="session")
+def r1_gamma_file(r1_tmp_path, prod5_gamma_simtel_path):
+    """
+    R1 file containing both waveforms and parameters from a gamma simulation set.
+    """
+    from ctapipe.tools.process import ProcessorTool
+
+    output = r1_tmp_path / "gamma.r1.h5"
+
+    argv = [
+        f"--input={prod5_gamma_simtel_path}",
+        f"--output={output}",
+        f"--DataWriter.write_r1_waveforms=True",
+        "--DataWriter.Contact.name=αℓℓ the äüöß",
+    ]
+    assert run_tool(ProcessorTool(), argv=argv, cwd=r1_tmp_path) == 0
+    return output