Getting Started with ctapipe¶

This hands-on was presented at the Paris CTA Consoritum meeting (K. Kosack)

Part 1: load and loop over data¶

[1]:

from ctapipe.io import EventSource
from ctapipe import utils
from matplotlib import pyplot as plt
import numpy as np
%matplotlib inline

[2]:

path = utils.get_dataset_path("gamma_prod5.simtel.zst")

[3]:

source = EventSource(path, max_events=5)

for event in source:
    print(event.count, event.index.event_id, event.simulation.shower.energy)

0 4009 0.07287972420454025 TeV
1 5101 1.7454713582992554 TeV
2 5103 1.7454713582992554 TeV
3 5104 1.7454713582992554 TeV
4 5105 1.7454713582992554 TeV

[4]:

event

[4]:

ctapipe.containers.ArrayEventContainer:
                       index.*: event indexing information with default None
                          r0.*: Raw Data with default None
                          r1.*: R1 Calibrated Data with default None
                         dl0.*: DL0 Data Volume Reduced Data with default None
                         dl1.*: DL1 Calibrated image with default None
                         dl2.*: DL2 reconstruction info with default None
                  simulation.*: Simulated Event Information with default None
                                with type <class
                                'ctapipe.containers.SimulatedEventContainer'>
                     trigger.*: central trigger information with default None
                         count: number of events processed with default 0
                    pointing.*: Array and telescope pointing positions with
                                default None
                 calibration.*: Container for calibration coefficients for the
                                current event with default None
                         mon.*: container for event-wise monitoring data (MON)
                                with default None
                        muon.*: Container for muon analysis results with default
                                None

[5]:

event.r1

[5]:

ctapipe.containers.R1Container:
                        tel[*]: map of tel_id to R1CameraContainer with default
                                None

[6]:

for event in EventSource(path, max_events=5):
    print(event.count, event.r1.tel.keys())

0 dict_keys([9, 14, 104])
1 dict_keys([26, 27, 29, 47, 53, 59, 69, 73, 121, 122, 124, 148, 162, 166])
2 dict_keys([82, 92, 175, 179])
3 dict_keys([17, 26, 27, 29, 43, 47, 53, 57, 69, 112, 121, 122, 124, 125, 128, 140, 144, 148, 162, 166])
4 dict_keys([3, 4, 8, 9, 14, 15, 23, 24, 25, 29, 32, 36, 42, 46, 52, 56, 103, 104, 109, 110, 118, 119, 120, 126, 127, 129, 130, 137, 139, 143, 161])

[7]:

event.r0.tel[3]

[7]:

ctapipe.containers.R0CameraContainer:
                      waveform: numpy array containing ADC samples(n_channels,
                                n_pixels, n_samples) with default None

[8]:

r0tel = event.r0.tel[3]

[9]:

r0tel.waveform

[9]:

array([[[432, 413, 395, ..., 382, 387, 382],
        [419, 420, 428, ..., 392, 396, 405],
        [381, 392, 413, ..., 375, 387, 387],
        ...,
        [391, 384, 385, ..., 379, 395, 404],
        [370, 376, 388, ..., 391, 383, 383],
        [393, 411, 413, ..., 406, 392, 396]],

       [[413, 396, 398, ..., 397, 401, 395],
        [392, 407, 403, ..., 403, 388, 399],
        [405, 403, 393, ..., 393, 400, 409],
        ...,
        [399, 406, 407, ..., 391, 405, 397],
        [401, 399, 396, ..., 395, 400, 388],
        [399, 393, 403, ..., 395, 407, 401]]], dtype=uint16)

[10]:

r0tel.waveform.shape

[10]:

(2, 1855, 40)

note that this is ($N_{channels}$, $N_{pixels}$, $N_{samples}$)

[11]:

plt.pcolormesh(r0tel.waveform[0])

[11]:

<matplotlib.collections.QuadMesh at 0x7f07b553c700>

../_images/tutorials_ctapipe_handson_13_1.png

[12]:

brightest_pixel = np.argmax(r0tel.waveform[0].sum(axis=1))
print(f"pixel {brightest_pixel} has sum {r0tel.waveform[0,1535].sum()}")

pixel 1831 has sum 15824

[13]:

plt.plot(r0tel.waveform[0,brightest_pixel], label="channel 0 (high-gain)")
plt.plot(r0tel.waveform[1,brightest_pixel], label="channel 1 (low-gain)")
plt.legend()

[13]:

<matplotlib.legend.Legend at 0x7f07b55f2130>

../_images/tutorials_ctapipe_handson_15_1.png

[14]:

from ipywidgets import interact

@interact
def view_waveform(chan=0, pix_id=brightest_pixel):
    plt.plot(r0tel.waveform[chan, pix_id])

try making this compare 2 waveforms

Part 2: Explore the instrument description¶

This is all well and good, but we don’t really know what camera or telescope this is… how do we get instrumental description info?

Currently this is returned inside the event (it will soon change to be separate in next version or so)

[15]:

subarray = source.subarray

[16]:

subarray

[16]:

SubarrayDescription(name='MonteCarloArray', n_tels=180)

[17]:

subarray.peek()

../_images/tutorials_ctapipe_handson_21_0.png

[18]:

subarray.to_table()

[18]:

Table length=180

tel_id	name	type	pos_x	pos_y	pos_z	camera_name	optics_name	camera_index	optics_index	tel_description
			m	m	m
int16	str5	str3	float32	float32	float32	str9	str5	int64	int64	str17
1	LST	LST	-20.643	-64.817	34.3	LSTCam	LST	2	1	LST_LST_LSTCam
2	LST	LST	79.993996	-0.768	29.4	LSTCam	LST	2	1	LST_LST_LSTCam
3	LST	LST	-19.396	65.2	31.0	LSTCam	LST	2	1	LST_LST_LSTCam
4	LST	LST	-120.033	1.151	33.1	LSTCam	LST	2	1	LST_LST_LSTCam
5	MST	MST	-0.017	-0.001	24.35	FlashCam	MST	1	2	MST_MST_FlashCam
6	MST	MST	-1.468	-151.221	31.0	FlashCam	MST	1	2	MST_MST_FlashCam
7	MST	MST	-3.1379998	-325.245	39.0	FlashCam	MST	1	2	MST_MST_FlashCam
8	MST	MST	1.4339999	151.22	25.0	FlashCam	MST	1	2	MST_MST_FlashCam
9	MST	MST	3.1039999	325.243	23.5	FlashCam	MST	1	2	MST_MST_FlashCam
...	...	...	...	...	...	...	...	...	...	...
171	ASTRI	SST	260.0	920.0	45.0	CHEC	ASTRI	0	0	SST_ASTRI_CHEC
172	ASTRI	SST	260.0	-920.0	65.0	CHEC	ASTRI	0	0	SST_ASTRI_CHEC
173	ASTRI	SST	-500.0	815.0	15.0	CHEC	ASTRI	0	0	SST_ASTRI_CHEC
174	ASTRI	SST	-500.0	-815.0	75.0	CHEC	ASTRI	0	0	SST_ASTRI_CHEC
175	ASTRI	SST	500.0	815.0	45.0	CHEC	ASTRI	0	0	SST_ASTRI_CHEC
176	ASTRI	SST	500.0	-815.0	53.0	CHEC	ASTRI	0	0	SST_ASTRI_CHEC
177	ASTRI	SST	-810.0	655.0	12.0	CHEC	ASTRI	0	0	SST_ASTRI_CHEC
178	ASTRI	SST	-810.0	-655.0	68.0	CHEC	ASTRI	0	0	SST_ASTRI_CHEC
179	ASTRI	SST	810.0	655.0	20.0	CHEC	ASTRI	0	0	SST_ASTRI_CHEC
180	ASTRI	SST	810.0	-655.0	41.0	CHEC	ASTRI	0	0	SST_ASTRI_CHEC

[19]:

subarray.tel[2]

[19]:

TelescopeDescription(type='LST', optics_name='LST', camera_name='LSTCam')

[20]:

subarray.tel[2].camera

[20]:

CameraDescription(name=LSTCam, geometry=LSTCam, readout=LSTCam)

[21]:

subarray.tel[2].optics

[21]:

OpticsDescription(name=LST, size_type=LST, reflector_shape=PARABOLIC, equivalent_focal_length=28.00 m, effective_focal_length=29.31 m, n_mirrors=1, mirror_area=386.73 m2)

[22]:

tel = subarray.tel[2]

[23]:

tel.camera

[23]:

CameraDescription(name=LSTCam, geometry=LSTCam, readout=LSTCam)

[24]:

tel.optics

[24]:

OpticsDescription(name=LST, size_type=LST, reflector_shape=PARABOLIC, equivalent_focal_length=28.00 m, effective_focal_length=29.31 m, n_mirrors=1, mirror_area=386.73 m2)

[25]:

tel.camera.geometry.pix_x

[25]:

$[0,~-0.037796701,~-0.047245475,~\dots,~0.67088033,~-0.45356484,~-0.50081024] \; \mathrm{m}$

[26]:

tel.camera.geometry.to_table()

[26]:

Table length=1855

pix_id	pix_x	pix_y	pix_area
	m	m	m2
int64	float64	float64	float64
0	0.0	0.0	0.002079326892271638
1	-0.03779670120038493	-0.03273242903676833	0.002079326892271638
2	-0.047245474963293455	0.01636666208397624	0.002079326892271638
3	-0.009448773762908525	0.04909909112074457	0.002079326892271638
4	0.03779670120038493	0.03273242903676833	0.002079326892271638
5	0.047245474963293455	-0.01636666208397624	0.002079326892271638
6	0.009448773762908525	-0.04909909112074457	0.002079326892271638
7	-0.07559330728842002	-0.06546483976983582	0.002079326892271638
8	-0.08504208105132854	-0.016365748649091242	0.002079326892271638
...	...	...	...
1845	-0.7086768843206072	0.9328863284767507	0.002079326892271638
1846	-0.6708803327659517	0.9656188254531994	0.002079326892271638
1847	0.45356483600883185	1.0801754621151207	0.002079326892271638
1848	0.5008102444966699	1.0638087511987853	0.002079326892271638
1849	1.1622417344092089	0.14728906047502402	0.002079326892271638
1850	1.1716905074681288	0.09818997301244675	0.002079326892271638
1851	0.7086768843206072	-0.9328863284767507	0.002079326892271638
1852	0.6708803327659517	-0.9656188254531994	0.002079326892271638
1853	-0.45356483600883185	-1.0801754621151207	0.002079326892271638
1854	-0.5008102444966699	-1.0638087511987853	0.002079326892271638

[27]:

tel.optics.mirror_area

[27]:

$386.73325 \; \mathrm{m^{2}}$

[28]:

from ctapipe.visualization import CameraDisplay

[29]:

disp = CameraDisplay(tel.camera.geometry)

../_images/tutorials_ctapipe_handson_33_0.png

[30]:

disp = CameraDisplay(tel.camera.geometry)
disp.image = r0tel.waveform[0,:,10]  # display channel 0, sample 0 (try others like 10)

../_images/tutorials_ctapipe_handson_34_0.png

** aside: ** show demo using a CameraDisplay in interactive mode in ipython rather than notebook

Part 3: Apply some calibration and trace integration¶

[31]:

from ctapipe.calib import CameraCalibrator

[32]:

calib = CameraCalibrator(subarray=subarray)

[33]:

for event in EventSource(path, max_events=5):
    calib(event) # fills in r1, dl0, and dl1
    print(event.dl1.tel.keys())

dict_keys([9, 14, 104])
dict_keys([26, 27, 29, 47, 53, 59, 69, 73, 121, 122, 124, 148, 162, 166])
dict_keys([82, 92, 175, 179])
dict_keys([17, 26, 27, 29, 43, 47, 53, 57, 69, 112, 121, 122, 124, 125, 128, 140, 144, 148, 162, 166])
dict_keys([3, 4, 8, 9, 14, 15, 23, 24, 25, 29, 32, 36, 42, 46, 52, 56, 103, 104, 109, 110, 118, 119, 120, 126, 127, 129, 130, 137, 139, 143, 161])

[34]:

event.dl1.tel[3]

[34]:

ctapipe.containers.DL1CameraContainer:
                         image: Numpy array of camera image, after waveform
                                extraction.Shape: (n_pixel) with default None as
                                a 1-D array with dtype float32
                     peak_time: Numpy array containing position of the peak of
                                the pulse as determined by the extractor. Shape:
                                (n_pixel, ) with default None as a 1-D array
                                with dtype float32
                    image_mask: Boolean numpy array where True means the pixel
                                has passed cleaning. Shape: (n_pixel, ) with
                                default None as a 1-D array with dtype bool
                      is_valid: True if image extraction succeeded, False if
                                failed or in the case of TwoPass methods, that
                                the first pass only was returned. with default
                                False
                    parameters: Image parameters with default None with type
                                <class
                                'ctapipe.containers.ImageParametersContainer'>

[35]:

dl1tel = event.dl1.tel[3]

[36]:

dl1tel.image.shape # note this will be gain-selected in next version, so will be just 1D array of 1855

[36]:

(1855,)

[37]:

dl1tel.peak_time

[37]:

array([27.381046, 17.746258, 18.80205 , ..., 11.64868 , 31.961287,
       29.717525], dtype=float32)

[38]:

CameraDisplay(tel.camera.geometry, image=dl1tel.image)

[38]:

<ctapipe.visualization.mpl_camera.CameraDisplay at 0x7f07b616b100>

../_images/tutorials_ctapipe_handson_44_1.png

[39]:

CameraDisplay(tel.camera.geometry, image=dl1tel.peak_time)

[39]:

<ctapipe.visualization.mpl_camera.CameraDisplay at 0x7f07b5793340>

../_images/tutorials_ctapipe_handson_45_1.png

Now for Hillas Parameters

[40]:

from ctapipe.image import hillas_parameters, tailcuts_clean

[41]:

image = dl1tel.image
mask = tailcuts_clean(tel.camera.geometry, image, picture_thresh=10, boundary_thresh=5)
mask

[41]:

array([False, False, False, ..., False, False, False])

[42]:

CameraDisplay(tel.camera.geometry, image=mask)

[42]:

<ctapipe.visualization.mpl_camera.CameraDisplay at 0x7f07b60ad100>

../_images/tutorials_ctapipe_handson_49_1.png

[43]:

cleaned = image.copy()
cleaned[~mask] = 0

[44]:

disp = CameraDisplay(tel.camera.geometry, image=cleaned)
disp.cmap = plt.cm.coolwarm
disp.add_colorbar()
plt.xlim(0.5, 1.0)
plt.ylim(-1.0, 0.0)

[44]:

(-1.0, 0.0)

../_images/tutorials_ctapipe_handson_51_1.png

[45]:

params = hillas_parameters(tel.camera.geometry, cleaned)
print(params)

{'intensity': 32.78351974487305,
 'kurtosis': 1.2333006676347844,
 'length': <Quantity 0.02219065 m>,
 'length_uncertainty': <Quantity 0.00093599 m>,
 'phi': <Angle -0.88747705 rad>,
 'psi': <Angle -1.56935711 rad>,
 'r': <Quantity 1.11337613 m>,
 'skewness': -0.2716153815520628,
 'width': <Quantity 0.01614423 m>,
 'width_uncertainty': <Quantity 0.00226475 m>,
 'x': <Quantity 0.70295289 m>,
 'y': <Quantity -0.86340237 m>}

[46]:

disp = CameraDisplay(tel.camera.geometry, image=cleaned)
disp.cmap = plt.cm.coolwarm
disp.add_colorbar()
plt.xlim(0.5, 1.0)
plt.ylim(-1.0, 0.0)
disp.overlay_moments(params, color='white', lw=2)

../_images/tutorials_ctapipe_handson_53_0.png

Part 4: Let’s put it all together:¶

loop over events, selecting only telescopes of the same type (e.g. LST:LSTCam)
for each event, apply calibration/trace integration
calculate Hillas parameters
write out all hillas paremeters to a file that can be loaded with Pandas

first let’s select only those telescopes with LST:LSTCam

[47]:

subarray.telescope_types

[47]:

(TelescopeDescription(type='SST', optics_name='ASTRI', camera_name='CHEC'),
 TelescopeDescription(type='LST', optics_name='LST', camera_name='LSTCam'),
 TelescopeDescription(type='MST', optics_name='MST', camera_name='NectarCam'),
 TelescopeDescription(type='MST', optics_name='MST', camera_name='FlashCam'))

[48]:

subarray.get_tel_ids_for_type("LST_LST_LSTCam")

[48]:

(1, 2, 3, 4)

Now let’s write out program

[49]:

data = utils.get_dataset_path("gamma_prod5.simtel.zst")
source = EventSource(data) # remove the max_events limit to get more stats

[50]:

for event in source:
    calib(event)

    for tel_id, tel_data in event.dl1.tel.items():
        tel = source.subarray.tel[tel_id]
        mask = tailcuts_clean(tel.camera.geometry, tel_data.image)
        if np.count_nonzero(mask) > 0:
            params = hillas_parameters(tel.camera.geometry[mask], tel_data.image[mask])

[51]:

from ctapipe.io import HDF5TableWriter

[52]:

with HDF5TableWriter(filename='hillas.h5', group_name='dl1', overwrite=True) as writer:

    source = EventSource(data, allowed_tels=[1,2,3,4],  max_events=10)
    for event in source:
        calib(event)

        for tel_id, tel_data in event.dl1.tel.items():
            tel = source.subarray.tel[tel_id]
            mask = tailcuts_clean(tel.camera.geometry, tel_data.image)
            params = hillas_parameters(tel.camera.geometry[mask], tel_data.image[mask])
            writer.write("hillas", params)

We can now load in the file we created and plot it¶

[53]:

!ls *.h5

hillas.h5

[54]:

import pandas as pd

hillas = pd.read_hdf("hillas.h5", key='/dl1/hillas')
hillas

[54]:

	intensity	skewness	kurtosis	x	y	r	phi	length	length_uncertainty	width	width_uncertainty	psi
0	47.098688	-0.530399	1.881643	0.695206	-0.847657	1.096282	-50.643096	0.032743	0.002240	0.026627	0.002372	-51.309393
1	126.314263	0.020218	1.742869	0.464446	-0.999899	1.102500	-65.085472	0.055256	0.002119	0.025090	0.001144	-67.386572

[55]:

_ = hillas.hist(figsize=(8,8))

../_images/tutorials_ctapipe_handson_66_0.png

If you do this yourself, chose a larger file to loop over more events to get better statistics