Merge branch 'master' into bokeh_plotter

* master: (60 commits)
  Add test that shows slicing breaks cam geom and fix it (cta-observatory#782)
  fix ctapipe build failure (cta-observatory#811)
  fix package name for yaml (should be pyyaml) (cta-observatory#810)
  Implement number of islands (cta-observatory#801)
  fixed ranges of cam-display so they correspond to fixed toymodel sims (cta-observatory#808)
  Fix unknown section example warning (cta-observatory#800)
  Fix timing parameters for case when there are negative values in image (cta-observatory#804)
  Update Timing Parameters (cta-observatory#799)
  speed up unit tests that use test_event fixture (cta-observatory#798)
  Add unit to h_max in HillasReconstructor (cta-observatory#797)
  Codacy code style improvements (cta-observatory#796)
  Minor changes: mostly deprecationwarning fixes (cta-observatory#787)
  Array plotting (cta-observatory#784)
  added a config file for github change-drafter plugin (cta-observatory#795)
  Simple HESS adaptations (cta-observatory#794)
  add test for sliced geometries for hillas calculation (cta-observatory#781)
  Impact intersection (cta-observatory#778)
  updated main documentation page (cta-observatory#792)
  Implement concentration image features (cta-observatory#791)
  Fix bad builds by changing channel name (missing pyqt package) (cta-observatory#793)
  ...

# Conflicts:
#	ctapipe/calib/camera/dl1.py

.github/release-drafter.yml

@@ -0,0 +1,8 @@
+template: |
+  ## What's Changed since $PREVIOUS_TAG
+
+  $CHANGES
+
+  ## Contributers
+
+  $CONTRIBUTERS

.travis.yml

@@ -54,7 +54,7 @@ install:
     - pip install codecov
     # ----- SST1M:
     - conda install protobuf
-    - pip install https://github.com/cta-sst-1m/protozfitsreader/archive/v0.44.4.tar.gz
+    - pip install https://github.com/cta-sst-1m/protozfitsreader/archive/v1.4.0.tar.gz
     # ----- end of SST1M
     # ----- target_software
     - conda install -c conda-forge cfitsio
@@ -72,6 +72,7 @@ script:
     - pytest --cov=ctapipe
     - ctapipe-info --version # print out the version string
     - travis-sphinx -v --outdir=docbuild build --source=docs/
+    - ./execute_ipynbs.py
 
 after_script:
     - source deactivate

AUTHORS

@@ -31,3 +31,89 @@ GernotMaier
 David Landriu
 labsaha
 Pierre Aubert
+Karl Kosack <[email protected]>
+Jason Watson <[email protected]>
+Dan Parsons <[email protected]>
+Jean Jacquemier <[email protected]>
+Tino Michael <[email protected]>
+Maximilian Nöthe <[email protected]>
+Christoph Deil <[email protected]>
+Alison Mitchell <[email protected]>
+justuszorn <[email protected]>
+Dominik Neise <[email protected]>
+Samuel Timothy Spencer <[email protected]>
+tino-michael <[email protected]>
+AMWMitchell <[email protected]>
+Kai Brügge <[email protected]>
+Raquel de los Reyes <[email protected]>
+Michele Mastropietro <[email protected]>
+Jeremie DECOCK <[email protected]>
+Abelardo Moralejo Olaizola <[email protected]>
+tialis <[email protected]>
+Markus Gaug <[email protected]>
+fvisconti <[email protected]>
+Wrijupan Bhattacharyya <[email protected]>
+bultako <[email protected]>
+Paolo Cumani <[email protected]>
+Ruben Lopez-Coto <[email protected]>
+Tristan Carel <[email protected]>
+Franca Cassol <[email protected]>
+nieto@talos <[email protected]>
+Tarek Hassan <[email protected]>
+Orel Gueta <[email protected]>
+Miguel Nievas <[email protected]>
+Michael Punch <[email protected]>
+Daniel Parsons <[email protected]>
+Cyril Alispach <[email protected]>
+Thomas Vuillaume <[email protected]>
+Konstantin Pfrang <[email protected]>
+GernotMaier <[email protected]>
+David Landriu <[email protected]>
+Pierre Aubert <[email protected]>
+labsaha <[email protected]>
+thomas gasparetto <[email protected]>
+thomasarmstrong <[email protected]>
+Julien Lefaucheur <[email protected]>
+Karl Kosack
+Jason Watson
+Dan Parsons
+Jean Jacquemier
+Tino Michael
+Maximilian Nöthe
+Christoph Deil
+Alison Mitchell
+justuszorn
+Dominik Neise
+Samuel Timothy Spencer
+tino-michael
+AMWMitchell
+Kai Brügge
+Raquel de los Reyes
+Michele Mastropietro
+Jeremie DECOCK
+Abelardo Moralejo Olaizola
+tialis
+Markus Gaug
+fvisconti
+Wrijupan Bhattacharyya
+bultako
+Paolo Cumani
+Ruben Lopez-Coto
+Tristan Carel
+Franca Cassol
+nieto@talos
+Tarek Hassan
+Orel Gueta
+Miguel Nievas
+Michael Punch
+Daniel Parsons
+Cyril Alispach
+Thomas Vuillaume
+Konstantin Pfrang
+GernotMaier
+David Landriu
+Pierre Aubert
+labsaha
+thomas gasparetto
+thomasarmstrong
+Julien Lefaucheur

README.rst

@@ -1,7 +1,8 @@
 =======
 ctapipe |teststatus| |codacy| |coverage| |conda| 
 =======
-.. |teststatus| image:: http://img.shields.io/travis/cta-observatory/ctapipe.svg?branch=master
+
+.. |teststatus| image:: https://travis-ci.org/cta-observatory/ctapipe.svg?branch=master
     :target: https://travis-ci.org/cta-observatory/ctapipe
     :alt: Test Status
 .. |codacy| image:: https://api.codacy.com/project/badge/Grade/d4f525fcb5d1421eb3a93dfa4eb5573d

ctapipe/analysis/camera/chargeresolution.py

@@ -56,10 +56,6 @@ def __init__(self, config=None, tool=None, **kwargs):
             Tool executable that is calling this component.
             Passes the correct logger to the component.
             Set to None if no Tool to pass.
-        reductor : ctapipe.calib.camera.reductors.Reductor
-            The reductor to use to reduce the waveforms in the event.
-            By default no data volume reduction is applied, and the dl0 samples
-            will equal the r1 samples.
         kwargs
         """
         super().__init__(config=config, parent=tool, **kwargs)

ctapipe/calib/camera/dl0.py

@@ -5,7 +5,7 @@
 transition exists as a conveniance in the pipepline and can be used to test
 data volume reduction methods inside the pipeline. By default, no data volume
 reduction is applied, and the DL0 samples are identical to the R1. However,
-if a reductor from `ctapipe.image.reductors` is passed to the
+if a reducer from `ctapipe.image.reducers` is passed to the
 `CameraDL0Reducer`, then the reduction will be applied.
 """
 from ctapipe.core import Component
@@ -27,18 +27,18 @@ class CameraDL0Reducer(Component):
         Tool executable that is calling this component.
         Passes the correct logger to the component.
         Set to None if no Tool to pass.
-    reductor : ctapipe.calib.camera.reductors.Reductor
-        The reductor to use to reduce the waveforms in the event.
+    reducer : ctapipe.calib.camera.reducer.Reducer
+        The reducer to use to reduce the waveforms in the event.
         By default no data volume reduction is applied, and the dl0 samples
         will equal the r1 samples.
     kwargs
     """
-    def __init__(self, config=None, tool=None, reductor=None, **kwargs):
+    def __init__(self, config=None, tool=None, reducer=None, **kwargs):
         super().__init__(config=config, parent=tool, **kwargs)
-        if reductor is None:
+        if reducer is None:
             self.log.info("Applying no data volume reduction in the "
                           "conversion from R1 to DL0")
-        self._reductor = reductor
+        self._reducer = reducer
         self._r1_empty_warn = False
 
     def check_r1_exists(self, event, telid):
@@ -84,8 +84,8 @@ def reduce(self, event):
         for telid in tels:
             r1 = event.r1.tel[telid].waveform
             if self.check_r1_exists(event, telid):
-                if self._reductor is None:
+                if self._reducer is None:
                     event.dl0.tel[telid].waveform = r1
                 else:
-                    reduction = self._reductor.reduce_waveforms(r1)
+                    reduction = self._reducer.reduce_waveforms(r1)
                     event.dl0.tel[telid].waveform = reduction

ctapipe/calib/camera/dl1.py

@@ -179,12 +179,7 @@ def get_correction(self, event, telid):
             # Don't apply correction when window_shift or window_width
             # does not exist in extractor, or when container does not have
             # a reference pulse shape
-            shape = event.dl0.tel[telid].waveform.shape
-            if shape.size != 3:
-                raise KeyError("this function should return 1 when "
-                               "channel is removed from dl0")
-            # TODO
-            return np.ones(shape[0])
+            return np.ones(event.dl0.tel[telid].waveform.shape[0])
 
     def calibrate(self, event):
         """

ctapipe/calib/camera/r1.py

@@ -14,7 +14,7 @@
 of the data.
 """
 from abc import abstractmethod
-
+import numpy as np
 from ...core import Component, Factory
 from ...core.traits import Unicode
 from ...io import EventSource
@@ -243,6 +243,7 @@ def __init__(self, config=None, tool=None, **kwargs):
             self.log.error(msg)
             raise
 
+        self._r1_wf = None
         self.tc = target_calib
         self.calibrator = None
         self.telid = 0
@@ -303,10 +304,13 @@ def real_calibrate(self, event):
                              'non-targetio event.')
 
         if self.check_r0_exists(event, self.telid):
-            samples = event.r0.tel[self.telid].waveform[0]
+            samples = event.r0.tel[self.telid].waveform
+            if self._r1_wf is None:
+                self._r1_wf = np.zeros(samples.shape, dtype=np.float32)
             fci = event.targetio.tel[self.telid].first_cell_ids
             r1 = event.r1.tel[self.telid].waveform[0]
-            self.calibrator.ApplyEvent(samples, fci, r1)
+            self.calibrator.ApplyEvent(samples[0], fci, self._r1_wf[0])
+            event.r1.tel[self.telid].waveform = self._r1_wf
 
 
 class CameraR1CalibratorFactory(Factory):

ctapipe/calib/camera/tests/test_calibrator.py

@@ -1,5 +1,5 @@
-from copy import deepcopy
 from numpy.testing import assert_allclose
+
 from ctapipe.calib.camera import (
     CameraCalibrator,
     HESSIOR1Calibrator,
@@ -10,14 +10,13 @@
 from ctapipe.utils import get_dataset_path
 
 
-def test_camera_calibrator(test_event):
-    event = deepcopy(test_event) # so we don't modify the test event
+def test_camera_calibrator(example_event):
     telid = 11
 
     calibrator = CameraCalibrator(r1_product="HESSIOR1Calibrator")
 
-    calibrator.calibrate(event)
-    image = event.dl1.tel[telid].image
+    calibrator.calibrate(example_event)
+    image = example_event.dl1.tel[telid].image
     assert_allclose(image[0, 0], -2.216, 1e-3)
 
 

ctapipe/calib/camera/tests/test_dl0.py

@@ -1,5 +1,3 @@
-from copy import deepcopy
-
 from numpy.testing import assert_almost_equal
 
 from ctapipe.calib.camera.dl0 import CameraDL0Reducer
@@ -11,22 +9,20 @@ def previous_calibration(event):
     r1.calibrate(event)
 
 
-def test_camera_dl0_reducer(test_event):
-    event = deepcopy(test_event)
-    previous_calibration(event)
+def test_camera_dl0_reducer(example_event):
+    previous_calibration(example_event)
     telid = 11
 
     reducer = CameraDL0Reducer()
-    reducer.reduce(event)
-    waveforms = event.dl0.tel[telid].waveform
+    reducer.reduce(example_event)
+    waveforms = example_event.dl0.tel[telid].waveform
     assert_almost_equal(waveforms[0, 0, 0], -0.091, 3)
 
 
-def test_check_r1_exists(test_event):
-    event = deepcopy(test_event)
+def test_check_r1_exists(example_event):
     telid = 11
-    previous_calibration(event)
+    previous_calibration(example_event)
     reducer = CameraDL0Reducer()
-    assert(reducer.check_r1_exists(event, telid) is True)
-    event.r1.tel[telid].waveform = None
-    assert(reducer.check_r1_exists(event, telid) is False)
+    assert (reducer.check_r1_exists(example_event, telid) is True)
+    example_event.r1.tel[telid].waveform = None
+    assert (reducer.check_r1_exists(example_event, telid) is False)

ctapipe/calib/camera/tests/test_dl1.py

@@ -1,5 +1,3 @@
-from copy import deepcopy
-
 from numpy.testing import assert_allclose
 
 from ctapipe.calib.camera.dl0 import CameraDL0Reducer
@@ -15,40 +13,46 @@ def previous_calibration(event):
     dl0.reduce(event)
 
 
-def test_integration_correction(test_event):
-    event = deepcopy(test_event)
+def test_integration_correction(example_event):
     telid = 11
     width = 7
     shift = 3
-    shape = event.mc.tel[telid].reference_pulse_shape
+    shape = example_event.mc.tel[telid].reference_pulse_shape
     n_chan = shape.shape[0]
-    step = event.mc.tel[telid].meta['refstep']
-    time_slice = event.mc.tel[telid].time_slice
+    step = example_event.mc.tel[telid].meta['refstep']
+    time_slice = example_event.mc.tel[telid].time_slice
     correction = integration_correction(n_chan, shape, step,
                                         time_slice, width, shift)
     assert_allclose(correction[0], 1.077, 1e-3)
 
 
-def test_camera_dl1_calibrator(test_event):
-    event = deepcopy(test_event)
-    previous_calibration(event)
+def test_integration_correction_no_ref_pulse(example_event):
+    previous_calibration(example_event)
+    telid = list(example_event.dl0.tel.keys())[0]
+    delattr(example_event, 'mc')
+    calibrator = CameraDL1Calibrator()
+    correction = calibrator.get_correction(example_event, telid)
+    assert correction[0] == 1
+
+
+def test_camera_dl1_calibrator(example_event):
+    previous_calibration(example_event)
     telid = 11
 
     calibrator = CameraDL1Calibrator()
 
-    correction = calibrator.get_correction(event, telid)
+    correction = calibrator.get_correction(example_event, telid)
     assert_allclose(correction[0], 1.077, 1e-3)
 
-    calibrator.calibrate(event)
-    image = event.dl1.tel[telid].image
+    calibrator.calibrate(example_event)
+    image = example_event.dl1.tel[telid].image
     assert_allclose(image[0, 0], -2.216, 1e-3)
 
 
-def test_check_dl0_exists(test_event):
-    event = deepcopy(test_event)
+def test_check_dl0_exists(example_event):
     telid = 11
-    previous_calibration(event)
+    previous_calibration(example_event)
     calibrator = CameraDL1Calibrator()
-    assert(calibrator.check_dl0_exists(event, telid) is True)
-    event.dl0.tel[telid].waveform = None
-    assert(calibrator.check_dl0_exists(event, telid) is False)
+    assert(calibrator.check_dl0_exists(example_event, telid) is True)
+    example_event.dl0.tel[telid].waveform = None
+    assert(calibrator.check_dl0_exists(example_event, telid) is False)