Merge branch 'master' of https://github.com/cta-observatory/ctapipe i…

…nto refactor/rename_data_writer_options

ctapipe/conftest.py

@@ -11,6 +11,15 @@
 from ctapipe.utils import get_dataset_path
 from ctapipe.utils.filelock import FileLock
 
+from pytest_astropy_header.display import PYTEST_HEADER_MODULES
+
+PYTEST_HEADER_MODULES.clear()
+PYTEST_HEADER_MODULES["eventio"] = "eventio"
+PYTEST_HEADER_MODULES["numpy"] = "numpy"
+PYTEST_HEADER_MODULES["scipy"] = "scipy"
+PYTEST_HEADER_MODULES["astropy"] = "astropy"
+PYTEST_HEADER_MODULES["numba"] = "numba"
+
 # names of camera geometries available on the data server
 camera_names = [
     "ASTRICam",
@@ -44,7 +53,8 @@ def _global_example_event():
 
     print("******************** LOAD TEST EVENT ***********************")
 
-    with SimTelEventSource(input_url=filename) as reader:
+    # FIXME: switch to prod5b+ file that contains effective focal length
+    with SimTelEventSource(input_url=filename, focal_length_choice="nominal") as reader:
         event = next(iter(reader))
 
     return event
@@ -59,7 +69,7 @@ def example_subarray():
 
     print("******************** LOAD TEST EVENT ***********************")
 
-    with SimTelEventSource(input_url=filename) as reader:
+    with SimTelEventSource(input_url=filename, focal_length_choice="nominal") as reader:
         return reader.subarray
 
 
@@ -84,7 +94,7 @@ def _subarray_and_event_gamma_off_axis_500_gev():
 
     path = get_dataset_path("lst_prod3_calibration_and_mcphotons.simtel.zst")
 
-    with SimTelEventSource(path) as source:
+    with SimTelEventSource(path, focal_length_choice="nominal") as source:
         it = iter(source)
         # we want the second event, first event is a corner clipper
         next(it)
@@ -353,6 +363,7 @@ def dl1_muon_file(dl1_tmp_path):
             "--write-dl1-images",
             "--DataWriter.write_dl1_parameters=False",
             "--DataWriter.Contact.name=αℓℓ the äüöß",
+            "--SimTelEventSource.focal_length_choice=nominal",
         ]
         assert run_tool(ProcessorTool(), argv=argv, cwd=dl1_tmp_path) == 0
         return output

ctapipe/coordinates/__init__.py

@@ -14,7 +14,12 @@
 import warnings
 from .telescope_frame import TelescopeFrame
 from .nominal_frame import NominalFrame
-from .ground_frames import GroundFrame, TiltedGroundFrame, project_to_ground
+from .ground_frames import (
+    GroundFrame,
+    TiltedGroundFrame,
+    project_to_ground,
+    EastingNorthingFrame,
+)
 from .camera_frame import CameraFrame, EngineeringCameraFrame
 
 
@@ -25,6 +30,7 @@
     "NominalFrame",
     "GroundFrame",
     "TiltedGroundFrame",
+    "EastingNorthingFrame",
     "MissingFrameAttributeWarning",
     "altaz_to_righthanded_cartesian",
     "project_to_ground",

ctapipe/coordinates/ground_frames.py

@@ -14,21 +14,25 @@
 - Tests Tests Tests!
 """
 import astropy.units as u
+from astropy.units.quantity import Quantity
 import numpy as np
 from astropy.coordinates import (
+    AltAz,
     BaseCoordinateFrame,
     CartesianRepresentation,
-    FunctionTransform,
     CoordinateAttribute,
-    AltAz,
+    FunctionTransform,
+    RepresentationMapping,
+    frame_transform_graph,
+    AffineTransform,
 )
-from astropy.coordinates import frame_transform_graph
 from numpy import cos, sin
 
 __all__ = [
     "GroundFrame",
     "TiltedGroundFrame",
     "project_to_ground",
+    "EastingNorthingFrame",
 ]
 
 
@@ -47,6 +51,25 @@ class GroundFrame(BaseCoordinateFrame):
     default_representation = CartesianRepresentation
 
 
+class EastingNorthingFrame(BaseCoordinateFrame):
+    """GroundFrame but in standard Easting/Northing coordinates instead of
+    SimTel/Corsika conventions
+
+    Frame attributes: None
+
+    """
+
+    default_representation = CartesianRepresentation
+
+    frame_specific_representation_info = {
+        CartesianRepresentation: [
+            RepresentationMapping("x", "easting"),
+            RepresentationMapping("y", "northing"),
+            RepresentationMapping("z", "height"),
+        ]
+    }
+
+
 class TiltedGroundFrame(BaseCoordinateFrame):
     """Tilted ground coordinate frame.  The tilted ground coordinate frame
     is a cartesian system describing the 2 dimensional projected
@@ -200,3 +223,34 @@ def project_to_ground(tilt_system):
     y_projected = y_initial - trans[2][1] * z_initial / trans[2][2]
 
     return GroundFrame(x=x_projected * unit, y=y_projected * unit, z=0 * unit)
+
+
+@frame_transform_graph.transform(FunctionTransform, GroundFrame, GroundFrame)
+def ground_to_ground(ground_coords, ground_frame):
+    """Null transform for going from ground to ground, since there are no
+    attributes of the GroundSystem"""
+    return ground_coords
+
+
+# Matrices for transforming between GroundFrame and EastingNorthingFrame
+NO_OFFSET = CartesianRepresentation(Quantity([0, 0, 0], u.m))
+GROUND_TO_EASTNORTH = np.asarray([[0, -1, 0], [1, 0, 0], [0, 0, 1]])
+
+
+@frame_transform_graph.transform(AffineTransform, GroundFrame, EastingNorthingFrame)
+def ground_to_easting_northing(ground_coords, eastnorth_frame):
+    """
+    convert GroundFrame points into eastings/northings for plotting purposes
+
+    """
+
+    return GROUND_TO_EASTNORTH, NO_OFFSET
+
+
+@frame_transform_graph.transform(AffineTransform, EastingNorthingFrame, GroundFrame)
+def easting_northing_to_ground(eastnorth_coords, ground_frame):
+    """
+    convert  eastings/northings back to GroundFrame
+
+    """
+    return GROUND_TO_EASTNORTH.T, NO_OFFSET

ctapipe/coordinates/tests/test_coordinates.py

@@ -72,7 +72,7 @@ def test_telescope_separation():
     tel1 = SkyCoord(fov_lon=0 * u.deg, fov_lat=0 * u.deg, frame=telescope_frame)
     tel2 = SkyCoord(fov_lon=0 * u.deg, fov_lat=1 * u.deg, frame=telescope_frame)
 
-    assert tel1.separation(tel2) == u.Quantity(1, u.deg)
+    assert u.isclose(tel1.separation(tel2), 1 * u.deg)
 
 
 def test_separation_is_the_same():
@@ -267,6 +267,7 @@ def test_camera_focal_length_array():
 
 
 def test_ground_frame_roundtrip():
+    """test transform from sky to ground roundtrip"""
     from ctapipe.coordinates import GroundFrame, TiltedGroundFrame
 
     normal = SkyCoord(alt=70 * u.deg, az=0 * u.deg, frame=AltAz())
@@ -275,6 +276,25 @@ def test_ground_frame_roundtrip():
 
     back = tilted.transform_to(GroundFrame())
 
-    assert u.isclose(coord.x, back.x)
-    assert u.isclose(coord.y, back.y)
-    assert u.isclose(coord.z, back.z)
+    assert u.isclose(coord.x, back.x, atol=1e-12 * u.m)
+    assert u.isclose(coord.y, back.y, atol=1e-12 * u.m)
+    assert u.isclose(coord.z, back.z, atol=1e-12 * u.m)
+
+
+def test_ground_to_eastnorth_roundtrip():
+    """Check Ground to EastingNorthing and the round-trip"""
+    from ctapipe.coordinates import GroundFrame, EastingNorthingFrame
+
+    ground = SkyCoord(
+        x=[1, 2, 3] * u.m, y=[-2, 5, 2] * u.m, z=[1, -1, 2] * u.m, frame=GroundFrame()
+    )
+    eastnorth = ground.transform_to(EastingNorthingFrame())
+    ground2 = eastnorth.transform_to(GroundFrame())
+
+    assert u.isclose(eastnorth.easting, [2, -5, -2] * u.m).all()
+    assert u.isclose(eastnorth.northing, [1, 2, 3] * u.m).all()
+    assert u.isclose(eastnorth.height, [1, -1, 2] * u.m).all()
+
+    assert u.isclose(ground.x, ground2.x).all()
+    assert u.isclose(ground.y, ground2.y).all()
+    assert u.isclose(ground.z, ground2.z).all()

ctapipe/core/component.py

@@ -2,6 +2,8 @@
 from abc import ABCMeta
 from inspect import isabstract
 from logging import getLogger
+from docutils.core import publish_parts
+from inspect import cleandoc
 
 from traitlets import TraitError
 from traitlets.config import Configurable
@@ -219,22 +221,45 @@ def _repr_html_(self):
         """nice HTML rep, with blue for non-default values"""
         traits = self.traits()
         name = self.__class__.__name__
+        docstring = (
+            publish_parts(cleandoc(self.__class__.__doc__), writer_name="html")[
+                "html_body"
+            ]
+            or "Undocumented"
+        )
         lines = [
+            "<div style='border:1px solid black; max-width: 700px; padding:2em'; word-wrap:break-word;>",
             f"<b>{name}</b>",
-            f"<p> {self.__class__.__doc__ or 'Undocumented!'} </p>",
+            f"<p> {docstring} </p>",
             "<table>",
+            "    <colgroup>",
+            "        <col span='1' style=' '>",
+            "        <col span='1' style='width: 20em;'>",
+            "        <col span='1' >",
+            "    </colgroup>",
+            "    <tbody>",
         ]
         for key, val in self.get_current_config()[name].items():
+            htmlval = (
+                str(val).replace("/", "/<wbr>").replace("_", "_<wbr>")
+            )  # allow breaking at boundary
+
             # traits of the current component
             if key in traits:
                 thehelp = f"{traits[key].help} (default: {traits[key].default_value})"
                 lines.append(f"<tr><th>{key}</th>")
                 if val != traits[key].default_value:
-                    lines.append(f"<td><span style='color:blue'>{val}</span></td>")
+                    lines.append(
+                        f"<td style='text-align: left;'><span style='color:blue; max-width:30em;'>{htmlval}</span></td>"
+                    )
                 else:
-                    lines.append(f"<td>{val}</td>")
-                lines.append(f'<td style="text-align:left"><i>{thehelp}</i></td></tr>')
+                    lines.append(f"<td style='text-align: left;'>{htmlval}</td>")
+                lines.append(
+                    f"<td style='text-align: left;'><i>{thehelp}</i></td></tr>"
+                )
+        lines.append("    </tbody>")
         lines.append("</table>")
+        lines.append("</div>")
         return "\n".join(lines)
 
 

ctapipe/core/container.py

@@ -77,7 +77,9 @@ def __repr__(self):
         if self.ndim is not None:
             desc += f" as a {self.ndim}-D array"
         if self.dtype is not None:
-            desc += f" with type {self.dtype}"
+            desc += f" with dtype {self.dtype}"
+        if self.type is not None:
+            desc += f" with type {self.type}"
 
         return desc
 
@@ -143,7 +145,7 @@ def validate(self, value):
 
 
 class DeprecatedField(Field):
-    """ used to mark which fields may be removed in next version """
+    """used to mark which fields may be removed in next version"""
 
     def __init__(self, default, description="", unit=None, ucd=None, reason=""):
         super().__init__(default=default, description=description, unit=unit, ucd=ucd)

ctapipe/core/tool.py

@@ -8,6 +8,8 @@
 from abc import abstractmethod
 from typing import Union
 import yaml
+from docutils.core import publish_parts
+from inspect import cleandoc
 
 try:
     import tomli as toml
@@ -401,30 +403,47 @@ def _repr_html_(self):
         """nice HTML rep, with blue for non-default values"""
         traits = self.traits()
         name = self.__class__.__name__
+        docstring = (
+            publish_parts(
+                cleandoc(self.__class__.__doc__ or self.description), writer_name="html"
+            )["html_body"]
+            or "Undocumented"
+        )
         lines = [
             f"<b>{name}</b>",
-            f"<p> {self.__class__.__doc__ or self.description} </p>",
+            f"<p> {docstring} </p>",
             "<table>",
+            "    <colgroup>",
+            "        <col span='1' style=' '>",
+            "        <col span='1' style='width: 20em;'>",
+            "        <col span='1' >",
+            "    </colgroup>",
+            "    <tbody>",
         ]
         for key, val in self.get_current_config()[name].items():
-            # after running setup, also the subcomponents are in the current config
-            # which are not in traits
-            if key not in traits:
-                continue
-
-            default = traits[key].default_value
-            thehelp = f"{traits[key].help} (default: {default})"
-            lines.append(f"<tr><th>{key}</th>")
-            if val != default:
-                lines.append(f"<td><span style='color:blue'>{val}</span></td>")
-            else:
-                lines.append(f"<td>{val}</td>")
-            lines.append(f'<td style="text-align:left"><i>{thehelp}</i></td></tr>')
-
+            htmlval = (
+                str(val).replace("/", "/<wbr>").replace("_", "_<wbr>")
+            )  # allow breaking at boundary
+
+            # traits of the current component
+            if key in traits:
+                thehelp = f"{traits[key].help} (default: {traits[key].default_value})"
+                lines.append(f"<tr><th>{key}</th>")
+                if val != traits[key].default_value:
+                    lines.append(
+                        f"<td style='text-align: left;'><span style='color:blue; max-width:30em;'>{htmlval}</span></td>"
+                    )
+                else:
+                    lines.append(f"<td style='text-align: left;'>{htmlval}</td>")
+                lines.append(
+                    f"<td style='text-align: left;'><i>{thehelp}</i></td></tr>"
+                )
+        lines.append("    </tbody>")
         lines.append("</table>")
-        lines.append("<p><i>Components:</i>")
+        lines.append("<p><b>Components:</b>")
         lines.append(", ".join([x.__name__ for x in self.classes]))
         lines.append("</p>")
+        lines.append("</div>")
 
         return "\n".join(lines)
 

ctapipe/image/__init__.py

@@ -45,7 +45,7 @@
     TwoPassWindowSum,
     extract_around_peak,
     extract_sliding_window,
-    neighbor_average_waveform,
+    neighbor_average_maximum,
     subtract_baseline,
     integration_correction,
 )
@@ -110,7 +110,7 @@
     "TwoPassWindowSum",
     "extract_around_peak",
     "extract_sliding_window",
-    "neighbor_average_waveform",
+    "neighbor_average_maximum",
     "subtract_baseline",
     "integration_correction",
     "DataVolumeReducer",