[5725] | 1 | #!/usr/bin/env python3 |
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| 2 | |
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| 3 | ########################################################################## |
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| 4 | # |
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| 5 | # pyLucia.py |
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| 6 | # |
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| 7 | # Visualisation tool |
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| 8 | # |
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| 9 | # Input: - timeline files produced by the OASIS coupler |
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| 10 | # ( load balancing measurement option required ) |
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| 11 | # - json or yaml configuration file (see example below ) |
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| 12 | # |
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| 13 | # Output: - timeline plot of OASIS coupling events |
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| 14 | # (in graphical format file and visulaisation GUI) |
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| 15 | # |
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| 16 | # Author : A. Piacentini (2020) |
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| 17 | # + E. Maisonnave (2020): Color blind friendly default palette |
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| 18 | # |
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| 19 | # |
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| 20 | # Poem lines : |
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| 21 | # |
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| 22 | # |
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| 23 | # |
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| 24 | ########################################################################## |
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| 25 | # |
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| 26 | # json config file example |
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| 27 | # |
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| 28 | ### |
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| 29 | # { |
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| 30 | # "Components":[ |
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| 31 | # {"Name":"Atmo", |
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| 32 | # "File":"timeline_atm.nc"}, |
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| 33 | # {"Name":"Ocean", |
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| 34 | # "File":"timeline_oce.nc"}, |
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| 35 | # {"Name":"IOserver", |
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| 36 | # "File":"timeline_ios.nc"} |
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| 37 | # ], |
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| 38 | # "Plots":{ |
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| 39 | # "Kind" : true, |
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| 40 | # "Field": true, |
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| 41 | # "Component": true |
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| 42 | # }, |
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| 43 | # "TimeRange":{ |
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| 44 | # "nominFrac":0.25, |
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| 45 | # "nomaxFrac":0.5, |
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| 46 | # "nominTime":20, |
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| 47 | # "nomaxTime":145 |
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| 48 | # }, |
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| 49 | # "Rendering":{ |
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| 50 | # "Display": true, |
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| 51 | # "File":"Lucia.png", |
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| 52 | # "EventsBounds": false, |
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| 53 | # "noPalette":"tab10" |
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| 54 | # }, |
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| 55 | # "Fields":["Heat","Rain","Love"] |
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| 56 | # } |
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| 57 | # |
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| 58 | # |
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| 59 | ########################################################################## |
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| 60 | # |
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| 61 | # yaml config file example |
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| 62 | # |
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| 63 | ### |
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| 64 | # --- |
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| 65 | # Components: |
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| 66 | # - Name: Atmo |
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| 67 | # File: timeline_pam_.nc |
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| 68 | # - Name: Ocean |
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| 69 | # File: timeline_pim_.nc |
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| 70 | # - Name: Xios |
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| 71 | # File: timeline_poum.nc |
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| 72 | # Plots: |
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| 73 | # Kind: True |
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| 74 | # Field: True |
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| 75 | # Component: True |
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| 76 | # #TimeRange: |
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| 77 | # # minFrac: 0.25 |
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| 78 | # # maxFrac: 0.5 |
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| 79 | # # minTime: 10 |
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| 80 | # # maxTime: 40 |
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| 81 | # Rendering: |
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| 82 | # Display: True |
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| 83 | # File: Lucia.png |
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| 84 | # EventsBounds: False |
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| 85 | # Fields: |
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| 86 | # - Heat |
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| 87 | # - Rain |
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| 88 | # - Love |
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| 89 | # |
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| 90 | ########################################################################## |
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| 91 | |
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| 92 | import netCDF4 |
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| 93 | try: |
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| 94 | import json |
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| 95 | has_json = True |
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| 96 | except: |
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| 97 | has_json = False |
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| 98 | try: |
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| 99 | import yaml |
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| 100 | has_yaml = True |
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| 101 | except: |
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| 102 | has_yaml = False |
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| 103 | import sys, os |
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| 104 | import time |
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| 105 | import numpy as np |
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| 106 | import matplotlib.pyplot as plt |
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| 107 | import matplotlib.collections |
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| 108 | from matplotlib.colors import LinearSegmentedColormap |
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| 109 | from matplotlib.backend_bases import MouseEvent |
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| 110 | import math |
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| 111 | |
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| 112 | if len(sys.argv) == 1: |
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| 113 | print(">>> Missing configuration file name") |
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| 114 | exit(1) |
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| 115 | |
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| 116 | config_ok = False |
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| 117 | if has_json: |
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| 118 | try: |
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| 119 | jf = open(sys.argv[1]) |
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| 120 | config = json.load(jf) |
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| 121 | config_ok = True |
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| 122 | except: |
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| 123 | pass |
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| 124 | if (not config_ok) and has_yaml: |
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| 125 | try: |
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| 126 | jf = open(sys.argv[1]) |
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| 127 | try: |
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| 128 | config = yaml.load(jf, Loader=yaml.FullLoader) |
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| 129 | config_ok = True |
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| 130 | except: |
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| 131 | try: |
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| 132 | config = yaml.load(jf) |
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| 133 | config_ok = True |
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| 134 | except: |
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| 135 | pass |
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| 136 | except: |
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| 137 | pass |
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| 138 | if not config_ok: |
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| 139 | print(">>> Problem loading configuration file {}".format(sys.argv[1])) |
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| 140 | exit(1) |
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| 141 | jf.close() |
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| 142 | |
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| 143 | initime = time.time() |
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| 144 | |
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| 145 | nbplots=sum([config["Plots"][i] for i in config["Plots"]]) |
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| 146 | if nbplots == 0: |
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| 147 | print("No plots selected") |
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| 148 | exit() |
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| 149 | |
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| 150 | |
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| 151 | files = [] |
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| 152 | cnam_in = [] |
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| 153 | for cp in config["Components"]: |
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| 154 | files.append(cp["File"]) |
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| 155 | cnam_in.append(cp["Name"]) |
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| 156 | |
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| 157 | if "Fields" in config: |
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| 158 | fieldlb = ["Oasis"]+config["Fields"] |
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| 159 | |
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| 160 | dofile = "File" in config["Rendering"] |
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| 161 | if dofile: |
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| 162 | outfile = config["Rendering"]["File"] |
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| 163 | if outfile: |
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| 164 | dofile = outfile.lower() != 'none' and outfile.lower() != 'no' |
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| 165 | else: |
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| 166 | dofile = False |
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| 167 | |
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| 168 | af_in = [netCDF4.Dataset(fi,'r') for fi in files] |
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| 169 | comp_id = [int(tf.getncattr('component_id'))-1 for tf in af_in] |
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| 170 | cnam = [cnam_in[id] for id in comp_id] |
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| 171 | af = [af_in[id] for id in comp_id] |
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| 172 | |
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| 173 | udpal = "Palette" in config["Rendering"] |
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| 174 | if udpal: |
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| 175 | udpalette = config["Rendering"]["Palette"] |
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| 176 | |
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| 177 | totprocs = -1 |
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| 178 | cprocs = [] |
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| 179 | fprocs = [] |
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| 180 | for i,tf in enumerate(af): |
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| 181 | timeini = time.time() |
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| 182 | nevents = len(tf.dimensions['nx']) |
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| 183 | nprocs = len(tf.dimensions['ny']) |
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| 184 | tstrt = tf.variables['timer_strt'][:,:].flatten() |
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| 185 | tstop = tf.variables['timer_stop'][:,:].flatten() |
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| 186 | if config["Plots"]["Kind"]: |
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| 187 | kind = tf.variables['kind'][:] |
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| 188 | kindlb = tf.variables['kind'].getncattr('flag_meanings').split() |
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| 189 | if config["Plots"]["Field"]: |
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| 190 | field = tf.variables['field'][:] |
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| 191 | if config["Plots"]["Component"]: |
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| 192 | compo = tf.variables['component'][:] |
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| 193 | tf.close() |
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| 194 | |
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| 195 | if config["Plots"]["Kind"]: |
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| 196 | lpkind = np.tile(kind,nprocs) |
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| 197 | if config["Plots"]["Field"]: |
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| 198 | lpfield = np.tile(field,nprocs) |
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| 199 | if config["Plots"]["Component"]: |
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| 200 | lpcompo = np.tile(compo,nprocs) |
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| 201 | |
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| 202 | procs = np.arange(nprocs)+totprocs+1 |
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| 203 | procs = np.repeat(procs,nevents) |
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| 204 | totprocs += nprocs |
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| 205 | cprocs.append(totprocs+1) |
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| 206 | fprocs.append(totprocs+1.5) |
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| 207 | |
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| 208 | polyx = np.array([tstrt,tstop,tstop,tstrt]).T |
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| 209 | polyy = np.array([procs+0.5,procs+0.5,procs+1.5,procs+1.5]).T |
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| 210 | lpolyxy = np.dstack((polyx[...,np.newaxis],polyy[...,np.newaxis])) |
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| 211 | |
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| 212 | if i == 0: |
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| 213 | if config["Plots"]["Kind"]: |
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| 214 | pkind = np.copy(lpkind) |
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| 215 | if config["Plots"]["Field"]: |
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| 216 | pfield = np.copy(lpfield) |
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| 217 | if config["Plots"]["Component"]: |
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| 218 | pcompo = np.copy(lpcompo) |
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| 219 | polyxy = np.copy(lpolyxy) |
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| 220 | else: |
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| 221 | if config["Plots"]["Kind"]: |
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| 222 | pkind = np.hstack((pkind,lpkind)) |
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| 223 | if config["Plots"]["Field"]: |
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| 224 | pfield = np.hstack((pfield,lpfield)) |
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| 225 | if config["Plots"]["Component"]: |
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| 226 | pcompo = np.hstack((pcompo,lpcompo)) |
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| 227 | polyxy = np.concatenate((polyxy,lpolyxy)) |
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| 228 | print('Loaded {} in {} sec.'.format(cnam[i],time.time()-timeini)) |
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| 229 | |
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| 230 | # Time range selection |
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| 231 | |
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| 232 | timeini = time.time() |
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| 233 | |
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| 234 | if config["Plots"]["Kind"]: |
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| 235 | minpkind = np.min(pkind) |
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| 236 | maxpkind = np.max(pkind) |
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| 237 | if config["Plots"]["Field"]: |
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| 238 | minpfield = np.min(pfield) |
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| 239 | maxpfield = np.max(pfield) |
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| 240 | if config["Plots"]["Component"]: |
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| 241 | minpcompo = np.min(pcompo) |
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| 242 | maxpcompo = np.max(pcompo) |
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| 243 | |
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| 244 | trange = np.max(polyxy[:,1,0])-np.min(polyxy[:,0,0]) |
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| 245 | print("The full trace spans {} sec. and contains {} events".format(trange,polyxy.shape[0])) |
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| 246 | |
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| 247 | uselimits = "TimeRange" in config |
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| 248 | if uselimits: |
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| 249 | if "minFrac" in config["TimeRange"]: |
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| 250 | tmin = np.min(polyxy[:,0,0]) + config["TimeRange"]["minFrac"] * trange |
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| 251 | else: |
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| 252 | if "minTime" in config["TimeRange"]: |
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| 253 | tmin = config["TimeRange"]["minTime"] |
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| 254 | else: |
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| 255 | tmin = np.min(polyxy[:,0,0]) |
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| 256 | if "maxFrac" in config["TimeRange"]: |
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| 257 | tmax = np.min(polyxy[:,0,0]) + config["TimeRange"]["maxFrac"] * trange |
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| 258 | else: |
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| 259 | if "maxTime" in config["TimeRange"]: |
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| 260 | tmax = config["TimeRange"]["maxTime"] |
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| 261 | else: |
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| 262 | tmax = np.max(polyxy[:,1,0]) |
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| 263 | else: |
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| 264 | tmin = np.min(polyxy[:,0,0]) |
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| 265 | tmax = np.max(polyxy[:,1,0]) |
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| 266 | tmin = float(math.floor(tmin)) |
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| 267 | tmax = float(math.ceil(tmax)) |
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| 268 | if uselimits: |
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| 269 | ti_msk = np.less_equal(polyxy[:,1,0],tmin) |
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| 270 | ti_msk = np.logical_or(ti_msk,np.greater_equal(polyxy[:,0,0],tmax)) |
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| 271 | |
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| 272 | if config["Plots"]["Kind"]: |
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| 273 | pkind = np.delete(pkind,ti_msk) |
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| 274 | if config["Plots"]["Field"]: |
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| 275 | pfield = np.delete(pfield,ti_msk) |
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| 276 | if config["Plots"]["Component"]: |
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| 277 | pcompo = np.delete(pcompo,ti_msk) |
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| 278 | polyxy = np.delete(polyxy,ti_msk,axis=0) |
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| 279 | print("The selection spans {} sec. between {} and {} and contains {} events".format(tmax-tmin,tmin,tmax,polyxy.shape[0])) |
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| 280 | print('Time range selection took {} sec'.format(str(time.time()-timeini))) |
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| 281 | |
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| 282 | |
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| 283 | # Plotting |
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| 284 | |
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| 285 | timeini = time.time() |
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| 286 | |
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| 287 | if nbplots == 1: |
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| 288 | figsz=(11.75,8.25) |
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| 289 | else: |
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| 290 | figsz=(8.25,11.75) |
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| 291 | |
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| 292 | fig=plt.figure(figsize=figsz, frameon=True) |
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| 293 | |
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| 294 | # Define default color blind friendly palette |
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| 295 | okabe_ito = ['#E69F00', '#56B4E9', '#009E73', '#F0E442', '#0072B2', '#D55E00', '#CC79A7', '#000000'] |
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| 296 | cmap_name = "mycolor" |
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| 297 | |
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| 298 | compolb = ['Oasis']+cnam |
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| 299 | compopc = [0]+cprocs |
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| 300 | plotnb = 0 |
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| 301 | |
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| 302 | if config["Plots"]["Kind"]: |
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| 303 | cm = LinearSegmentedColormap.from_list(cmap_name, okabe_ito, N=10) |
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| 304 | if udpal: |
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| 305 | palette = udpalette # 'tab10' # or 'Paired' |
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| 306 | else : |
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| 307 | palette = cm |
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| 308 | plotnb += 1 |
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| 309 | kind_ax = plt.subplot(nbplots*100+10+plotnb) |
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| 310 | kind_ax.set_ylim([0.5,totprocs+1.5]) |
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| 311 | kind_ax.set_xlim([tmin,tmax]) |
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| 312 | kind_pc = matplotlib.collections.PolyCollection(polyxy,pickradius=0.0) |
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| 313 | kind_pc.set_array(pkind) |
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| 314 | kind_pc.set_clim([minpkind-.5,maxpkind+.5]) |
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| 315 | cmap = plt.get_cmap(palette, maxpkind-minpkind+1) |
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| 316 | cbar = plt.colorbar(kind_pc, ticks=np.arange(minpkind,maxpkind+1)) |
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| 317 | kind_pc.set_cmap(cmap) |
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| 318 | |
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| 319 | plt.hlines(fprocs[:-1],tmin,tmax,colors='black',linestyles='dashed', linewidth=0.8) |
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| 320 | kind_ax.add_collection(kind_pc) |
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| 321 | kind_ax.set_title('KIND') |
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| 322 | cbar.ax.set_yticklabels(kindlb[minpkind:maxpkind+1]) |
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| 323 | for i,label in enumerate(compolb[1:],start=1): |
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| 324 | kind_ax.text(tmax*1.005, |
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| 325 | compopc[i-1]+(compopc[i]-compopc[i-1])/2, |
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| 326 | compolb[i],{'ha': 'left', 'va': 'center'}, |
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| 327 | rotation = 60) |
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| 328 | |
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| 329 | if config["Plots"]["Field"]: |
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| 330 | cm = LinearSegmentedColormap.from_list(cmap_name, okabe_ito, N=len(fieldlb)) |
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| 331 | if udpal: |
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| 332 | palette = udpalette # 'tab10' # or 'Paired' |
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| 333 | else : |
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| 334 | palette = cm |
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| 335 | plotnb += 1 |
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| 336 | field_ax = plt.subplot(nbplots*100+10+plotnb) |
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| 337 | field_ax.set_ylim([0.5,totprocs+1.5]) |
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| 338 | field_ax.set_xlim([tmin,tmax]) |
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| 339 | field_pc = matplotlib.collections.PolyCollection(polyxy,pickradius=0.0) |
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| 340 | field_pc.set_array(pfield) |
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| 341 | field_pc.set_clim([minpfield-.5,maxpfield+.5]) |
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| 342 | cmap = plt.get_cmap(palette, len(fieldlb)) |
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| 343 | cbar = plt.colorbar(field_pc, ticks=np.arange(len(fieldlb))) |
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| 344 | field_pc.set_cmap(cmap) |
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| 345 | |
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| 346 | plt.hlines(fprocs[:-1],tmin,tmax,colors='black',linestyles='dashed', linewidth=0.8) |
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| 347 | field_ax.add_collection(field_pc) |
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| 348 | field_ax.set_title('FIELD') |
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| 349 | if "Fields" in config: |
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| 350 | cbar.ax.set_yticklabels(fieldlb) |
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| 351 | for i,label in enumerate(compolb[1:],start=1): |
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| 352 | field_ax.text(tmax*1.005, |
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| 353 | compopc[i-1]+(compopc[i]-compopc[i-1])/2, |
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| 354 | compolb[i],{'ha': 'left', 'va': 'center'}, |
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| 355 | rotation = 60) |
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| 356 | |
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| 357 | if config["Plots"]["Component"]: |
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| 358 | cm = LinearSegmentedColormap.from_list(cmap_name, okabe_ito, N=len(compolb)) |
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| 359 | if udpal: |
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| 360 | palette = udpalette # 'tab10' # or 'Paired' |
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| 361 | else : |
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| 362 | palette = cm |
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| 363 | plotnb += 1 |
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| 364 | compo_ax = plt.subplot(nbplots*100+10+plotnb) |
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| 365 | compo_ax.set_ylim([0.5,totprocs+1.5]) |
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| 366 | compo_ax.set_xlim([tmin,tmax]) |
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| 367 | compo_pc = matplotlib.collections.PolyCollection(polyxy,pickradius=0.0) |
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| 368 | compo_pc.set_array(pcompo) |
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| 369 | compo_pc.set_clim([-.5,len(compolb)-.5]) |
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| 370 | cmap = plt.get_cmap(palette, len(compolb)) |
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| 371 | cbar = plt.colorbar(compo_pc, ticks=np.arange(len(compolb))) |
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| 372 | compo_pc.set_cmap(cmap) |
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| 373 | |
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| 374 | plt.hlines(fprocs[:-1],tmin,tmax,colors='black',linestyles='dashed', linewidth=0.8) |
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| 375 | compo_ax.add_collection(compo_pc) |
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| 376 | compo_ax.set_title('COMPONENT') |
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| 377 | cbar.ax.set_yticklabels(compolb) |
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| 378 | for i,label in enumerate(compolb[1:],start=1): |
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| 379 | compo_ax.text(tmax*1.005, |
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| 380 | compopc[i-1]+(compopc[i]-compopc[i-1])/2, |
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| 381 | compolb[i],{'ha': 'left', 'va': 'center'}, |
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| 382 | rotation = 60) |
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| 383 | |
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| 384 | plt.subplots_adjust(left=0.07,right=1.05,bottom=0.03,top=0.95,wspace=0.0,hspace=0.2) |
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| 385 | |
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| 386 | print('Plot preparation took {} sec'.format(str(time.time()-timeini))) |
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| 387 | |
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| 388 | if dofile: |
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| 389 | timeini = time.time() |
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| 390 | plt.savefig(outfile,bbox_inches='tight') |
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| 391 | print('File output took {} sec'.format(str(time.time()-timeini))) |
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| 392 | print('Overall time {} sec'.format(str(time.time()-initime))) |
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| 393 | |
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| 394 | if config["Rendering"]["Display"]: |
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| 395 | if "EventsBounds" not in config["Rendering"]: |
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| 396 | config["Rendering"]["EventsBounds"] = False |
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| 397 | if config["Rendering"]["EventsBounds"]: |
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| 398 | if config["Plots"]["Kind"]: |
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| 399 | kind_pc.set_edgecolor('black') |
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| 400 | kind_pc.set_linewidth(0.3) |
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| 401 | if config["Plots"]["Field"]: |
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| 402 | field_pc.set_edgecolor('black') |
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| 403 | field_pc.set_linewidth(0.3) |
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| 404 | if config["Plots"]["Component"]: |
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| 405 | compo_pc.set_edgecolor('black') |
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| 406 | compo_pc.set_linewidth(0.3) |
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| 407 | |
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| 408 | class pseudo_mouse: |
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| 409 | def __init__(self,x,y): |
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| 410 | self.x = x |
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| 411 | self.y = y |
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| 412 | |
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| 413 | if config["Plots"]["Kind"]: |
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| 414 | def format_coord_kind(x, y): |
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| 415 | comp = compolb[min(np.searchsorted(fprocs,y)+1,len(compolb)-1)] |
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| 416 | ip = min(max(1,int(round(y))),compopc[-1]) |
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| 417 | proc = ip-1 - compopc[np.searchsorted(fprocs,y)] |
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| 418 | px, py = kind_pc.get_transform().transform((x,y)) |
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| 419 | cont, ind = kind_pc.contains(pseudo_mouse(px,py)) |
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| 420 | if cont: |
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| 421 | return 'Time: {:.3f}, Resource: {:.0f}, Component: {}, Rank: {:.0f}, Kind: {}'.format(x, ip, comp, proc, kindlb[pkind[ind['ind'][0]]]) |
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| 422 | else: |
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| 423 | return 'Time: {:.3f}, Resource: {:.0f}, Component: {}, Rank: {:.0f}'.format(x, ip, comp, proc) |
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| 424 | |
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| 425 | kind_ax.format_coord = format_coord_kind |
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| 426 | if config["Plots"]["Field"]: |
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| 427 | def format_coord_field(x, y): |
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| 428 | comp = compolb[min(np.searchsorted(fprocs,y)+1,len(compolb)-1)] |
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| 429 | ip = min(max(1,int(round(y))),compopc[-1]) |
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| 430 | proc = ip-1 - compopc[np.searchsorted(fprocs,y)] |
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| 431 | px, py = field_pc.get_transform().transform((x,y)) |
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| 432 | cont, ind = field_pc.contains(pseudo_mouse(px,py)) |
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| 433 | if cont: |
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| 434 | return 'Time: {:.3f}, Resource: {:.0f}, Component: {}, Rank: {:.0f}, Field: {}'.format(x, ip, comp, proc, fieldlb[pfield[ind['ind'][0]]]) |
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| 435 | else: |
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| 436 | return 'Time: {:.3f}, Resource: {:.0f}, Component: {}, Rank: {:.0f}'.format(x, ip, comp, proc) |
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| 437 | |
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| 438 | field_ax.format_coord = format_coord_field |
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| 439 | if config["Plots"]["Component"]: |
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| 440 | def format_coord_compo(x, y): |
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| 441 | comp = compolb[min(np.searchsorted(fprocs,y)+1,len(compolb)-1)] |
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| 442 | ip = min(max(1,int(round(y))),compopc[-1]) |
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| 443 | proc = ip-1 - compopc[np.searchsorted(fprocs,y)] |
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| 444 | px, py = compo_pc.get_transform().transform((x,y)) |
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| 445 | cont, ind = compo_pc.contains(pseudo_mouse(px,py)) |
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| 446 | if cont: |
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| 447 | return 'Time: {:.3f}, Resource: {:.0f}, Component: {}, Rank: {:.0f}, Comp: {}'.format(x, ip, comp, proc, compolb[pcompo[ind['ind'][0]]]) |
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| 448 | else: |
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| 449 | return 'Time: {:.3f}, Resource: {:.0f}, Component: {}, Rank: {:.0f}'.format(x, ip, comp, proc) |
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| 450 | |
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| 451 | compo_ax.format_coord = format_coord_compo |
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| 452 | plt.show() |
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