RUBIX pipeline#
RUBIX is designed as a linear pipeline, where the individual functions are called and constructed as a pipeline. This allows as to execude the whole data transformation from a cosmological hydrodynamical simulation of a galaxy to an IFU cube in two lines of code. This notebook shows, how to execute the pipeline. To see, how the pipeline is execuded in small individual steps per individual function, we refer to the notebook rubix_pipeline_stepwise.ipynb.
How to use the Pipeline#
Define a
configSetup the
pipeline yamlRun the RUBIX pipeline
Do science with the mock-data
Step 1: Config#
The config contains all the information needed to run the pipeline. Those are run specfic configurations. Currently we just support Illustris as simulation, but extensions to other simulations (e.g. NIHAO) are planned.
For the config you can choose the following options:
pipeline: you specify the name of the pipeline that is stored in the yaml file in rubix/config/pipeline_config.ymllogger: RUBIX has implemented a logger to report the user, what is happening during the pipeline execution and give warningsdata - args - particle_type: load only stars particle (“particle_type”: [“stars”]) or only gas particle (“particle_type”: [“gas”]) or both (“particle_type”: [“stars”,”gas”])data - args - simulation: choose the Illustris simulation (e.g. “simulation”: “TNG50-1”)data - args - snapshot: which time step of the simulation (99 for present day)data - args - save_data_path: set the path to save the downloaded Illustris datadata - load_galaxy_args - id: define, which Illustris galaxy is downloadeddata - load_galaxy_args - reuse: if True, if in th esave_data_path directory a file for this galaxy id already exists, the downloading is skipped and the preexisting file is useddata - subset: only a defined number of stars/gas particles is used and stored for the pipeline. This may be helpful for quick testingsimulation - name: currently only IllustrisTNG is supportedsimulation - args - path: where the data is stored and how the file will be namedoutput_path: where the hdf5 file is stored, which is then the input to the RUBIX pipelinetelescope - name: define the telescope instrument that is observing the simulation. Some telescopes are predefined, e.g. MUSE. If your instrument does not exist predefined, you can easily define your instrument in rubix/telescope/telescopes.yamltelescope - psf: define the point spread function that is applied to the mock datatelescope - lsf: define the line spread function that is applied to the mock datatelescope - noise: define the noise that is applied to the mock datacosmology: specify the cosmology you want to use, standard for RUBIX is “PLANCK15”galaxy - dist_z: specify at which redshift the mock-galaxy is observedgalaxy - rotation: specify the orientation of the galaxy. You can set the types edge-on or face-on or specify the angles alpha, beta and gamma as rotations around x-, y- and z-axisssp - template: specify the simple stellar population lookup template to get the stellar spectrum for each stars particle. In RUBIX frequently “BruzualCharlot2003” is used.
#NBVAL_SKIP
import matplotlib.pyplot as plt
from rubix.core.pipeline import RubixPipeline
import os
config = {
"pipeline":{"name": "calc_ifu"},
"logger": {
"log_level": "DEBUG",
"log_file_path": None,
"format": "%(asctime)s - %(name)s - %(levelname)s - %(message)s",
},
"data": {
"name": "IllustrisAPI",
"args": {
"api_key": os.environ.get("ILLUSTRIS_API_KEY"),
"particle_type": ["stars"],
"simulation": "TNG50-1",
"snapshot": 99,
"save_data_path": "data",
},
"load_galaxy_args": {
"id": 14,
"reuse": True,
},
"subset": {
"use_subset": True,
"subset_size": 1000,
},
},
"simulation": {
"name": "IllustrisTNG",
"args": {
"path": "data/galaxy-id-14.hdf5",
},
},
"output_path": "output",
"telescope":
{"name": "MUSE",
"psf": {"name": "gaussian", "size": 5, "sigma": 0.6},
"lsf": {"sigma": 0.5},
"noise": {"signal_to_noise": 1,"noise_distribution": "normal"},},
"cosmology":
{"name": "PLANCK15"},
"galaxy":
{"dist_z": 0.1,
"rotation": {"type": "edge-on"},
},
"ssp": {
"template": {
"name": "BruzualCharlot2003"
},
},
}
2024-11-18 13:19:01,768 - rubix - INFO -
___ __ _____ _____ __
/ _ \/ / / / _ )/ _/ |/_/
/ , _/ /_/ / _ |/ /_> <
/_/|_|\____/____/___/_/|_|
2024-11-18 13:19:01,769 - rubix - INFO - Rubix version: 0.0.post134+g6444210.d20241106
2024-11-18 13:19:01,770 - rubix - WARNING - python-fsps is not installed. Please install it to use this function. Install using pip install fsps and check the installation page: https://dfm.io/python-fsps/current/installation/ for more details. Especially, make sure to set all necessary environment variables.
Step 2: Pipeline yaml#
To run the RUBIX pipeline, you need a yaml file (stored in rubix/config/pipeline_config.yml) that defines which functions are used during the execution of the pipeline. This shows the example pipeline yaml to compute a stellar IFU cube.
calc_ifu:
Transformers:
rotate_galaxy:
name: rotate_galaxy
depends_on: null
args: []
kwargs:
type: "face-on"
filter_particles:
name: filter_particles
depends_on: rotate_galaxy
args: []
kwargs: {}
spaxel_assignment:
name: spaxel_assignment
depends_on: filter_particles
args: []
kwargs: {}
reshape_data:
name: reshape_data
depends_on: spaxel_assignment
args: []
kwargs: {}
calculate_spectra:
name: calculate_spectra
depends_on: reshape_data
args: []
kwargs: {}
scale_spectrum_by_mass:
name: scale_spectrum_by_mass
depends_on: calculate_spectra
args: []
kwargs: {}
doppler_shift_and_resampling:
name: doppler_shift_and_resampling
depends_on: scale_spectrum_by_mass
args: []
kwargs: {}
calculate_datacube:
name: calculate_datacube
depends_on: doppler_shift_and_resampling
args: []
kwargs: {}
convolve_psf:
name: convolve_psf
depends_on: calculate_datacube
args: []
kwargs: {}
convolve_lsf:
name: convolve_lsf
depends_on: convolve_psf
args: []
kwargs: {}
apply_noise:
name: apply_noise
depends_on: convolve_lsf
args: []
kwargs: {}
Ther is one thing you have to know about the naming of the functions in this yaml: To use the functions inside the pipeline, the functions have to be called exactly the same as they are returned from the core module function!
Step 3: Run the pipeline#
After defining the config and the pipeline_config you can simply run the whole pipeline by these two lines of code.
#NBVAL_SKIP
pipe = RubixPipeline(config)
rubixdata = pipe.run()
/home/annalena/rubix/rubix/telescope/factory.py:24: UserWarning: No telescope config provided, using default stored in /home/annalena/rubix/rubix/telescope/telescopes.yaml
warnings.warn(
2024-11-18 13:19:03,591 - rubix - INFO - Getting rubix data...
2024-11-18 13:19:03,592 - rubix - INFO - Rubix galaxy file already exists, skipping conversion
2024-11-18 13:19:03,777 - rubix - INFO - Centering stars particles
2024-11-18 13:19:05,835 - rubix - WARNING - The Subset value is set in config. Using only subset of size 1000 for stars
2024-11-18 13:19:05,839 - rubix - INFO - Data loaded with 1000 star particles and 0 gas particles.
2024-11-18 13:19:05,839 - rubix - INFO - Data loaded with 48 properties.
2024-11-18 13:19:05,840 - rubix - DEBUG - Data: RubixData(galaxy=Galaxy(redshift=2.220446049250313e-16, center=array([11413.86337268, 35893.86374042, 32027.01940138]), halfmassrad_stars=7.727193253526112), stars=StarsData(coords=Array([[ 0.01953125, 0.12109375, 0.1953125 ],
[ 3.305664 , 1.5234375 , -1.8144531 ],
[ 1.4316406 , 5.6953125 , -1.4589844 ],
...,
[-0.22949219, -0.0546875 , -0.02148438],
[15.157227 , -4.2460938 , 4.4746094 ],
[14.027344 , -0.015625 , -2.1054688 ]], dtype=float32), velocity=Array([[ 2.2396517e-15, 2.4131075e-15, -4.0351599e-15],
[ 9.0712782e-17, 8.7445301e-15, -6.1377769e-15],
[-4.2026344e-15, 1.9314719e-15, 7.7893150e-17],
...,
[ 5.8114825e-16, -1.3959399e-16, 3.1129105e-15],
[ 8.0419468e-16, 2.5377044e-15, -2.7024722e-15],
[-2.7399760e-15, 2.3714432e-15, -2.5337364e-15]], dtype=float32), mass=Array([103706.484, 73743.086, 70998.35 , 85374.91 , 82220.21 ,
88501.25 , 138703.16 , 98413.58 , 114730.28 , 110815.65 ,
106835.34 , 82952.766, 55514.266, 45093.457, 119139.87 ,
99465.29 , 81894.88 , 99098.49 , 121604.28 , 73959.84 ,
81568.74 , 77949.09 , 63735.67 , 83705.78 , 88831.94 ,
94049.12 , 128544.5 , 111424.14 , 85921.4 , 81257.164,
120619.51 , 91774.32 , 146891.14 , 112913.516, 86486.46 ,
95861.19 , 106234.39 , 99594.17 , 84475.86 , 88601.766,
123305.914, 92989.03 , 80892.92 , 116025.11 , 92752.86 ,
133442.92 , 58536.78 , 75977.53 , 107455.69 , 102766.82 ,
69256.67 , 90629.86 , 113887.055, 94529.17 , 98055.66 ,
145879.19 , 79203.086, 60170.086, 101019.29 , 96633.11 ,
89888.5 , 119878.25 , 106734.414, 71238.766, 107306.516,
52672.63 , 93005.36 , 95320.91 , 52186.527, 130619.73 ,
70907.23 , 83238.39 , 60344.555, 126573.48 , 119303.85 ,
106244.78 , 117947.8 , 90023.53 , 130132.05 , 154391.06 ,
108217.01 , 108079.766, 70043.76 , 97929.53 , 135604.33 ,
100191.43 , 141311.58 , 66223.63 , 77482.83 , 117216.625,
94993.87 , 81198.43 , 103967.98 , 119972.016, 63966.664,
84706.984, 93145.51 , 91789.97 , 138873.17 , 97771.766,
78426.984, 82272.12 , 95569.23 , 111268.99 , 69179. ,
69945.21 , 93762.21 , 77290.44 , 99038.3 , 102819.836,
121096.664, 86104.16 , 115770.76 , 71230.914, 102111.65 ,
127704.99 , 100001.27 , 122007.21 , 98949.87 , 108799.62 ,
45367.477, 87785.29 , 85747.45 , 91871.68 , 129286.016,
157948.77 , 99121.81 , 65377.97 , 76733.04 , 98953.19 ,
143347.9 , 85568.734, 114235.586, 116849.25 , 70448.96 ,
79609.516, 82454.75 , 76978.05 , 72914.914, 82279.41 ,
108404.42 , 102680.914, 75665.92 , 95232.195, 104924.44 ,
161324.4 , 93109.43 , 106213.39 , 69224.35 , 91687.19 ,
94972.766, 100404.36 , 64690.22 , 108578.83 , 96024.46 ,
87660.586, 71993.32 , 92670.36 , 118846.34 , 88499.09 ,
121490.41 , 106298.35 , 87116.16 , 84743.04 , 141193.3 ,
150384.14 , 94293.445, 80642.33 , 75813.09 , 80358.47 ,
90295.125, 67994.05 , 89223.81 , 131639.22 , 92760.51 ,
109354.41 , 56792.426, 57390.582, 90733.32 , 90823.99 ,
76613.03 , 133907.92 , 72256.62 , 99349.07 , 121417.46 ,
113764.77 , 61972.594, 87527.555, 74782.195, 79731.51 ,
118405.48 , 86716.1 , 73361.21 , 95322.21 , 80881.914,
125435.164, 136370.03 , 55025.703, 95667.33 , 115835.6 ,
90640.85 , 105854.73 , 131222.5 , 80385.945, 82782.75 ,
71727.4 , 58484.926, 85653.836, 75960.25 , 93423.33 ,
88612.37 , 91737.984, 88118.95 , 128495.055, 62555.863,
84572.78 , 68407.47 , 101724.195, 92262.75 , 90828.14 ,
102337.19 , 105714.914, 70140.5 , 87052.44 , 87405.01 ,
103563.17 , 117247.99 , 112633.99 , 76865.91 , 109124.72 ,
94626.97 , 61512.06 , 161041.08 , 112796.664, 116881.27 ,
88419.26 , 73282.375, 99186.67 , 90680.75 , 87184.65 ,
87714.12 , 107003.234, 122223.24 , 113636.85 , 71009.87 ,
119632.67 , 129031.82 , 97809.13 , 100149.53 , 133759.66 ,
72218.52 , 105218.48 , 91820.16 , 116302.01 , 120828.23 ,
66523.85 , 95621.99 , 121244.63 , 140439.47 , 86387.14 ,
92905.98 , 103331.92 , 73082.016, 80244.8 , 104475.71 ,
62483.504, 104800.89 , 90167.516, 128359.22 , 76597.09 ,
62095.586, 66116.41 , 122153.47 , 107697.555, 105410.26 ,
95080.22 , 72365.89 , 96533.89 , 90342.31 , 104238.81 ,
164011.89 , 73281.19 , 77675.83 , 103286.61 , 92131.945,
79492.234, 103175.414, 91831.54 , 74050.64 , 122732.36 ,
97924.805, 75816.555, 106413.65 , 89908.84 , 140560.66 ,
77965.2 , 121917.23 , 121019.54 , 89423.484, 83513.23 ,
96105.7 , 122074.25 , 86650.43 , 63591.887, 101602.74 ,
107806.39 , 108742.555, 94687.79 , 73712.37 , 89079.66 ,
79479.555, 62432.58 , 85436.15 , 139891.31 , 88966.83 ,
122616.48 , 64631.375, 92514.47 , 97164.49 , 113423.41 ,
45712.81 , 134149.28 , 78758.06 , 137630.05 , 146748.3 ,
107416.984, 70812.12 , 89469.23 , 64776.766, 108347.99 ,
93304.42 , 116929.016, 123408.125, 97897.84 , 88075.08 ,
77202.62 , 79226.24 , 86912.29 , 87327.734, 77936.13 ,
104750.51 , 105350.86 , 80376.09 , 77657.15 , 117382.95 ,
90714.26 , 86512.28 , 53954.14 , 95636.65 , 116473.32 ,
81456.1 , 103083.73 , 94223.055, 104848.16 , 70106.12 ,
120994.48 , 82119.76 , 116493.86 , 74859.914, 94340.836,
75720.14 , 75011.336, 129385.84 , 102488.25 , 94594.695,
114385.22 , 78330.77 , 112164.625, 107609.805, 118911.195,
61688.555, 110717.164, 110507.234, 89349.44 , 102691.125,
88979.84 , 103455.71 , 92368.15 , 95294.35 , 59448.61 ,
74083.42 , 100776.664, 66297.5 , 94908.48 , 91836.984,
93289.81 , 90402.59 , 80194.81 , 95950.65 , 89125.49 ,
134062. , 75205.12 , 98685.984, 71394.34 , 76059.44 ,
79033.55 , 69241.84 , 55896.543, 109183.26 , 58432.984,
83764.76 , 72993.99 , 124567.836, 93393.69 , 106451.43 ,
114471.18 , 63391.39 , 84105.04 , 82900.2 , 114317.4 ,
121177.24 , 95629.414, 80614.95 , 132495.34 , 143995.67 ,
57900.36 , 83696.82 , 135735.75 , 101862.63 , 59422.336,
79934.445, 79776.41 , 88711.46 , 94004.16 , 118422.9 ,
54291.27 , 106824.33 , 88080.96 , 83281.29 , 144200.1 ,
121297.48 , 92788.68 , 71587.86 , 71693.83 , 79290.7 ,
100440.28 , 110222.07 , 95124.12 , 91107.91 , 94596.56 ,
75741.375, 48096.395, 113035.07 , 99908.4 , 111697.62 ,
93423.266, 126490.25 , 73289.72 , 85496.56 , 100744.2 ,
100672.234, 84681.38 , 117332.234, 113048.16 , 89121.586,
128322.1 , 94701.75 , 95786.97 , 125852.85 , 80056.19 ,
122384.125, 102609.586, 101684.03 , 58844.95 , 97872.625,
102129.7 , 99610.26 , 112077.45 , 79936.3 , 95699.16 ,
94128.02 , 109341.73 , 70908.95 , 100342.234, 109257.484,
128694.734, 40169.094, 103509.96 , 50607.918, 98546.914,
78877.09 , 109361.26 , 101660.93 , 71001.63 , 89517.19 ,
113630.25 , 72683.11 , 95688.58 , 71497.89 , 71388.85 ,
78820.04 , 81286.6 , 62205.195, 110225.84 , 83703.58 ,
98517.15 , 60689.215, 80968.52 , 104963.695, 59065.91 ,
97302.87 , 86533.45 , 80444.84 , 89597.516, 69351.96 ,
103612.15 , 84449.63 , 86945.01 , 110613.78 , 91861.61 ,
129047.57 , 112316.64 , 131168.36 , 105665.69 , 83869.02 ,
98838.48 , 91249.914, 72762.31 , 92261.95 , 91180.35 ,
105055.83 , 99701.25 , 109368.98 , 94266.46 , 91842.75 ,
97174.195, 69864.81 , 111580.67 , 73000.48 , 116982.64 ,
97039.51 , 96735.54 , 82170.31 , 76772.4 , 71373.914,
93942.95 , 137930.89 , 73491.305, 45522.305, 72374.484,
98368.984, 69098.63 , 90592.67 , 107103.74 , 155540. ,
113036.85 , 138120.8 , 91674.29 , 90031.555, 63334.51 ,
124379.86 , 75419.94 , 74885.7 , 115947.67 , 81708.83 ,
144293.94 , 95200.266, 88370.79 , 144164.12 , 94730.836,
107308.83 , 167453.17 , 95462.266, 81414.38 , 98816.28 ,
117500.266, 106049.414, 142834.23 , 140332.02 , 55017.43 ,
108087.39 , 93460.63 , 116811.555, 79292.55 , 81632.055,
86589.23 , 94405.03 , 66433.164, 97646.76 , 86446.08 ,
104727.164, 139598.11 , 95858.75 , 101942.39 , 93054.94 ,
93679.945, 67439.805, 72444.99 , 110807.77 , 74849.98 ,
83353.97 , 100162.94 , 112900.91 , 102895.64 , 113664.266,
83197.42 , 63005.555, 90588.914, 92638.6 , 74182.07 ,
81099.38 , 102329.945, 72664.53 , 100871.68 , 117361.1 ,
101378.945, 101945.266, 97662.08 , 113930.7 , 76603.96 ,
101375.45 , 136521.72 , 104288.27 , 83660.7 , 60995.26 ,
69730.45 , 80142.25 , 103045.85 , 66783.56 , 119343.69 ,
94661.75 , 89706.875, 89695.37 , 84743.04 , 79419.92 ,
140119.45 , 129846.63 , 76032.55 , 103887.63 , 71698.29 ,
102096.18 , 90808.49 , 64946.12 , 127416.14 , 76151.29 ,
92710.81 , 79896.25 , 75339.48 , 112669.984, 93495.586,
90814.48 , 101308.23 , 118459.984, 119426.266, 83594.17 ,
57298.395, 114240.125, 86101.25 , 128737.82 , 74623.414,
114252.56 , 89449.62 , 78304.305, 79548.66 , 118591.83 ,
72985.625, 105386.86 , 111986.7 , 118763.41 , 93660.33 ,
87847.32 , 109689.42 , 76494.89 , 97502.62 , 130443.945,
86120.92 , 96781.445, 82427.7 , 81910.42 , 83105.836,
78988.875, 79368.38 , 89549.516, 72950.87 , 103732.28 ,
83353.055, 126053.445, 113373.66 , 91909.93 , 66809.305,
121739.266, 74398.3 , 99692.12 , 124474.56 , 102081.9 ,
119546.28 , 84958.47 , 106927.4 , 111892.76 , 112320.1 ,
110633.14 , 119503.48 , 59511.8 , 106983.055, 135738.12 ,
66386.984, 100819.52 , 110342.87 , 106715. , 59176.992,
86112.836, 126786.71 , 65583.85 , 103620.88 , 81640.16 ,
71154.37 , 116278.39 , 77073.414, 93145.48 , 139995.9 ,
84292.93 , 75677.74 , 85022.34 , 77055.58 , 78970.75 ,
106841.43 , 98551.36 , 77637.7 , 162873.17 , 58680.06 ,
74162.45 , 125901.73 , 93518.54 , 114768.2 , 98853.58 ,
98435.64 , 93291.266, 90789.625, 91608.21 , 98526.66 ,
88778.94 , 118339.29 , 88254.664, 114547.96 , 106083.414,
86156.58 , 96394.805, 125383.17 , 123755.484, 67516.75 ,
117885.08 , 93608.42 , 69339.62 , 97533.18 , 105075.2 ,
51938.926, 69717.9 , 147494.34 , 77910.3 , 121322.48 ,
61264.09 , 75327.64 , 128240.94 , 81286.87 , 90709.99 ,
67640.93 , 123451.73 , 68001.734, 122384.25 , 126877.87 ,
117985.664, 78287.3 , 123450.836, 110381.2 , 99409.75 ,
99479.65 , 103106.3 , 114135.875, 61217.176, 101965.65 ,
103414.09 , 135256.56 , 121449.45 , 57194.496, 91295.305,
102966.25 , 97068.51 , 98563.59 , 86400.22 , 106492.01 ,
101443.16 , 100645.34 , 94879.56 , 107999.74 , 73824.07 ,
64908.94 , 76843.07 , 95568.61 , 93093.64 , 102083.984,
61437.625, 68695.61 , 134152.98 , 68294.305, 51138.94 ,
150865.58 , 80437.695, 135526.67 , 122776. , 96554.89 ,
90112.58 , 74083.195, 127246.52 , 127033.06 , 96882.98 ,
80026.875, 80930.34 , 119916.57 , 85523.445, 99842.32 ,
83888.79 , 87155.62 , 92761.164, 89285.36 , 55887.156,
118178.26 , 84300.805, 61603.375, 79690.805, 101982.266,
127704.62 , 95493.33 , 96061. , 111350.79 , 48169.156,
97612.9 , 93948.13 , 83332.766, 80944.54 , 117019.625,
88740.27 , 102357.37 , 78393.75 , 115471.49 , 97645.01 ,
145121.5 , 66540.836, 124100.04 , 92683.49 , 92247.15 ,
111519.766, 87818.586, 99559.21 , 78815.93 , 105439.84 ,
110950.19 , 120310.42 , 105773.82 , 106410.71 , 84529.35 ,
107824.87 , 96241.516, 91291.43 , 104016.55 , 86593.66 ,
126362.52 , 156541.92 , 133678.94 , 74640.31 , 79126.53 ,
121217.89 , 108098.664, 87873.484, 115539.945, 80791.67 ,
61723.016, 102573.586, 101548.695, 66237.93 , 84449.63 ,
66494.016, 115187.12 , 82161.68 , 77564.26 , 110085.71 ,
104859.82 , 96234.55 , 89221.74 , 121338.97 , 58262.71 ,
110025.23 , 80679.61 , 78503.43 , 123528.52 , 86552.13 ,
90678.35 , 78640.84 , 167147.02 , 73780.76 , 94175.42 ,
118392.98 , 119783.14 , 80135.125, 104012.75 , 63262.258,
104551.086, 92350.83 , 104334.375, 90642.86 , 87326.836,
85779.14 , 62959.336, 82141.125, 130775.91 , 102592.1 ,
87474.766, 85142.87 , 102306.13 , 81084.805, 112683.664,
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9.949278 , 10.23471 , 9.00513 , 6.617514 , 5.044818 ,
6.56374 , 5.9834123 , 3.5904546 , 11.3228 , 7.0224977 ,
6.482805 , 4.836316 , 7.1764603 , 7.464969 , 6.149914 ,
10.794198 , 8.284809 , 6.2515545 , 10.667138 , 6.75501 ,
11.453717 , 9.969853 , 10.0127325 , 10.170054 , 10.493387 ,
4.8003626 , 8.3354845 , 6.730339 , 10.137119 , 5.8983393 ,
6.7651076 , 6.335283 , 6.3443866 , 8.822149 , 7.7916365 ,
10.2301 , 6.1745396 , 5.74316 , 6.153449 , 9.903646 ,
7.9665174 , 4.52647 , 3.4685907 , 6.275379 , 9.25705 ,
6.6490984 , 5.6148434 , 9.808211 , 9.210986 , 11.577889 ,
10.392145 , 8.682878 , 11.49146 , 9.186821 , 4.2905927 ,
5.9688873 , 0.7820431 , 3.319744 , 6.399899 , 2.0419753 ,
4.984504 , 10.069207 , 5.433458 , 7.972048 , 9.592842 ,
6.690865 , 7.133813 , 6.3338213 , 7.44604 , 7.5983734 ], dtype=float32), pixel_assignment=None, spatial_bin_edges=None, mask=None, spectra=None, datacube=None), gas=GasData(coords=None, velocity=None, mass=None, density=None, internal_energy=None, metallicity=None, sfr=None, electron_abundance=None, pixel_assignment=None, spatial_bin_edges=None, mask=None, spectra=None, datacube=None))
2024-11-18 13:19:05,854 - rubix - INFO - Setting up the pipeline...
2024-11-18 13:19:05,854 - rubix - DEBUG - Pipeline Configuration: {'Transformers': {'rotate_galaxy': {'name': 'rotate_galaxy', 'depends_on': None, 'args': [], 'kwargs': {'type': 'face-on'}}, 'filter_particles': {'name': 'filter_particles', 'depends_on': 'rotate_galaxy', 'args': [], 'kwargs': {}}, 'spaxel_assignment': {'name': 'spaxel_assignment', 'depends_on': 'filter_particles', 'args': [], 'kwargs': {}}, 'reshape_data': {'name': 'reshape_data', 'depends_on': 'spaxel_assignment', 'args': [], 'kwargs': {}}, 'calculate_spectra': {'name': 'calculate_spectra', 'depends_on': 'reshape_data', 'args': [], 'kwargs': {}}, 'scale_spectrum_by_mass': {'name': 'scale_spectrum_by_mass', 'depends_on': 'calculate_spectra', 'args': [], 'kwargs': {}}, 'doppler_shift_and_resampling': {'name': 'doppler_shift_and_resampling', 'depends_on': 'scale_spectrum_by_mass', 'args': [], 'kwargs': {}}, 'calculate_datacube': {'name': 'calculate_datacube', 'depends_on': 'doppler_shift_and_resampling', 'args': [], 'kwargs': {}}, 'convolve_psf': {'name': 'convolve_psf', 'depends_on': 'calculate_datacube', 'args': [], 'kwargs': {}}, 'convolve_lsf': {'name': 'convolve_lsf', 'depends_on': 'convolve_psf', 'args': [], 'kwargs': {}}, 'apply_noise': {'name': 'apply_noise', 'depends_on': 'convolve_lsf', 'args': [], 'kwargs': {}}}}
2024-11-18 13:19:05,855 - rubix - DEBUG - Roataion Type found: edge-on
2024-11-18 13:19:05,856 - rubix - INFO - Calculating spatial bin edges...
/home/annalena/rubix/rubix/telescope/factory.py:24: UserWarning: No telescope config provided, using default stored in /home/annalena/rubix/rubix/telescope/telescopes.yaml
warnings.warn(
2024-11-18 13:19:05,872 - rubix - INFO - Getting cosmology...
/home/annalena/rubix/rubix/telescope/factory.py:24: UserWarning: No telescope config provided, using default stored in /home/annalena/rubix/rubix/telescope/telescopes.yaml
warnings.warn(
2024-11-18 13:19:06,447 - rubix - INFO - Calculating spatial bin edges...
/home/annalena/rubix/rubix/telescope/factory.py:24: UserWarning: No telescope config provided, using default stored in /home/annalena/rubix/rubix/telescope/telescopes.yaml
warnings.warn(
2024-11-18 13:19:06,462 - rubix - INFO - Getting cosmology...
2024-11-18 13:19:06,477 - rubix - DEBUG - Method not defined, using default method: cubic
/home/annalena/rubix/rubix/telescope/factory.py:24: UserWarning: No telescope config provided, using default stored in /home/annalena/rubix/rubix/telescope/telescopes.yaml
warnings.warn(
2024-11-18 13:19:06,565 - rubix - DEBUG - SSP Wave: (842,)
/home/annalena/rubix/rubix/telescope/factory.py:24: UserWarning: No telescope config provided, using default stored in /home/annalena/rubix/rubix/telescope/telescopes.yaml
warnings.warn(
/home/annalena/rubix/rubix/telescope/factory.py:24: UserWarning: No telescope config provided, using default stored in /home/annalena/rubix/rubix/telescope/telescopes.yaml
warnings.warn(
2024-11-18 13:19:07,124 - rubix - INFO - Assembling the pipeline...
2024-11-18 13:19:07,124 - rubix - INFO - Compiling the expressions...
2024-11-18 13:19:07,125 - rubix - INFO - Running the pipeline on the input data...
2024-11-18 13:19:07,133 - rubix - INFO - Rotating galaxy with alpha=90.0, beta=0.0, gamma=0.0
2024-11-18 13:19:07,237 - rubix - INFO - Filtering particles outside the aperture...
2024-11-18 13:19:07,242 - rubix - INFO - Assigning particles to spaxels...
2024-11-18 13:19:07,262 - rubix - INFO - Calculating IFU cube...
2024-11-18 13:19:07,262 - rubix - DEBUG - Input shapes: Metallicity: 1, Age: 1
2024-11-18 13:19:07,432 - rubix - DEBUG - Calculation Finished! Spectra shape: (1, 1000, 842)
2024-11-18 13:19:07,432 - rubix - INFO - Scaling Spectra by Mass...
2024-11-18 13:19:07,437 - rubix - INFO - Doppler shifting and resampling stellar spectra...
2024-11-18 13:19:07,438 - rubix - DEBUG - Doppler Shifted SSP Wave: (1, 1000, 842)
2024-11-18 13:19:07,438 - rubix - DEBUG - Telescope Wave Seq: (3721,)
2024-11-18 13:19:07,494 - rubix - INFO - Calculating Data Cube...
2024-11-18 13:19:07,496 - rubix - DEBUG - Datacube Shape: (25, 25, 3721)
2024-11-18 13:19:07,497 - rubix - INFO - Convolving with PSF...
2024-11-18 13:19:07,499 - rubix - INFO - Convolving with LSF...
2024-11-18 13:19:07,503 - rubix - INFO - Applying noise to datacube with signal to noise ratio: 1 and noise distribution: normal
2024-11-18 13:19:09,684 - rubix - INFO - Pipeline run completed in 3.83 seconds.
Step 4: Mock-data#
Now we have our final datacube and can use the mock-data to do science. Here we have a quick look in the optical wavelengthrange of the mock-datacube and show the spectra of a central spaxel and a spatial image.
#NBVAL_SKIP
import jax.numpy as jnp
wave = pipe.telescope.wave_seq
# get the indices of the visible wavelengths of 4000-8000 Angstroms
visible_indices = jnp.where((wave >= 4000) & (wave <= 8000))
This is how you can access the spectrum of an individual spaxel, the wavelength can be accessed via pipe.wave_seq
#NBVAL_SKIP
wave = pipe.telescope.wave_seq
spectra = rubixdata.stars.datacube # Spectra of all stars
print(spectra.shape)
plt.plot(wave, spectra[12,12,:])
(25, 25, 3721)
[<matplotlib.lines.Line2D at 0x7f29901beb30>]
Plot a spacial image of the data cube
#NBVAL_SKIP
# get the spectra of the visible wavelengths from the ifu cube
visible_spectra = rubixdata.stars.datacube[:, :, visible_indices[0]]
#visible_spectra.shape
# Sum up all spectra to create an image
image = jnp.sum(visible_spectra, axis = 2)
plt.imshow(image, origin="lower", cmap="inferno")
plt.colorbar()
<matplotlib.colorbar.Colorbar at 0x7f2990551120>
DONE!#
Congratulations, you have sucessfully run the RUBIX pipeline to create your own mock-observed IFU datacube! Now enjoy playing around with the RUBIX pipeline and enjoy doing amazing science with RUBIX :)