tobac example: Tracking isolated convection based on updraft velocity and total condensate

This example notebook demonstrates the use of tobac to track isolated deep convective clouds in cloud-resolving model simulation output based on vertical velocity and total condensate mixing ratio.

The simulation results used in this example were performed as part of the ACPC deep convection intercomparison case study (http://acpcinitiative.org/Docs/ACPC_DCC_Roadmap_171019.pdf) with WRF using the Morrison microphysics scheme.

The data used in this example is downloaded from “zenodo link” automatically as part of the notebooks (This only has to be done once for all the tobac example notebooks).

Import libraries:

[1]:

# Import libraries:
import xarray
import numpy as np
import pandas as pd
import os
from six.moves import urllib
from glob import glob

import matplotlib.pyplot as plt
%matplotlib inline

[2]:

# Import tobac itself:
import tobac

[3]:

#Disable a couple of warnings:
import warnings
warnings.filterwarnings('ignore', category=UserWarning, append=True)
warnings.filterwarnings('ignore', category=RuntimeWarning, append=True)
warnings.filterwarnings('ignore', category=FutureWarning, append=True)
warnings.filterwarnings('ignore',category=pd.io.pytables.PerformanceWarning)
Download and load example data:
The actual dowloading is only necessary once for all example notebooks.
[4]:

data_out='../'

[6]:

# # Download the data: This only has to be done once for all tobac examples and can take a while
# file_path='https://zenodo.org/record/3195910/files/climate-processes/tobac_example_data-v1.0.1.zip'
# #file_path='http://zenodo..'
# tempfile='temp.zip'
# print('start downloading data')
# request=urllib.request.urlretrieve(file_path,tempfile)
# print('start extracting data')
# shutil.unpack_archive(tempfile,data_out)
# # zf = zipfile.ZipFile(tempfile)
# # zf.extractall(data_out)
# os.remove(tempfile)
# print('data extracted')

Load Data from downloaded file:

[7]:

data_file_W_mid_max = os.path.join(data_out,'*','data','Example_input_midlevelUpdraft.nc')
data_file_W_mid_max = glob(data_file_W_mid_max)[0]
data_file_TWC = os.path.join(data_out,'*','data','Example_input_Condensate.nc')
data_file_TWC = glob(data_file_TWC)[0]

[8]:

W_mid_max=xarray.open_dataset(data_file_W_mid_max)['w']
TWC=xarray.open_dataset(data_file_TWC)['twc']

[9]:

# Display information about the two cubes for vertical velocity and total condensate mixing ratio:
display(W_mid_max)
display(TWC)
Show/Hide data repr Show/Hide attributes
xarray.DataArray
'w'
  • time: 47
  • south_north: 198
  • west_east: 198
  • ...
    [1842588 values with dtype=float32]
    • time
      (time)
      datetime64[ns]
      2013-06-19T20:05:00 ... 2013-06-19T23:55:00
      axis :
      T
      standard_name :
      time
      array(['2013-06-19T20:05:00.000000000', '2013-06-19T20:10:00.000000000',
       '2013-06-19T20:15:00.000000000', '2013-06-19T20:20:00.000000000',
       '2013-06-19T20:25:00.000000000', '2013-06-19T20:30:00.000000000',
       '2013-06-19T20:35:00.000000000', '2013-06-19T20:40:00.000000000',
       '2013-06-19T20:45:00.000000000', '2013-06-19T20:50:00.000000000',
       '2013-06-19T20:55:00.000000000', '2013-06-19T21:00:00.000000000',
       '2013-06-19T21:05:00.000000000', '2013-06-19T21:10:00.000000000',
       '2013-06-19T21:15:00.000000000', '2013-06-19T21:20:00.000000000',
       '2013-06-19T21:25:00.000000000', '2013-06-19T21:30:00.000000000',
       '2013-06-19T21:35:00.000000000', '2013-06-19T21:40:00.000000000',
       '2013-06-19T21:45:00.000000000', '2013-06-19T21:50:00.000000000',
       '2013-06-19T21:55:00.000000000', '2013-06-19T22:00:00.000000000',
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       '2013-06-19T22:45:00.000000000', '2013-06-19T22:50:00.000000000',
       '2013-06-19T22:55:00.000000000', '2013-06-19T23:00:00.000000000',
       '2013-06-19T23:05:00.000000000', '2013-06-19T23:10:00.000000000',
       '2013-06-19T23:15:00.000000000', '2013-06-19T23:20:00.000000000',
       '2013-06-19T23:25:00.000000000', '2013-06-19T23:30:00.000000000',
       '2013-06-19T23:35:00.000000000', '2013-06-19T23:40:00.000000000',
       '2013-06-19T23:45:00.000000000', '2013-06-19T23:50:00.000000000',
       '2013-06-19T23:55:00.000000000'], dtype='datetime64[ns]')
    • south_north
      (south_north)
      int64
      281 282 283 284 ... 475 476 477 478
      units :
      1
      long_name :
      south_north
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    • west_east
      (west_east)
      int64
      281 282 283 284 ... 475 476 477 478
      units :
      1
      long_name :
      west_east
      array([281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294,
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       477, 478])
    • bottom_top_stag
      ()
      int64
      ...
      bounds :
      bottom_top_stag_bnds
      units :
      1
      long_name :
      bottom_top_stag
      array(39)
    • latitude
      (south_north, west_east)
      float32
      ...
      units :
      degrees_north
      standard_name :
      latitude
      FieldType :
      104
      MemoryOrder :
      XY
      description :
      LATITUDE, SOUTH IS NEGATIVE
      stagger :
      array([[29.62032 , 29.620296, 29.620296, ..., 29.615593, 29.615551, 29.615501],
       [29.624874, 29.624874, 29.624859, ..., 29.620167, 29.620113, 29.620071],
       [29.629444, 29.629429, 29.629429, ..., 29.624718, 29.624683, 29.624634],
       ...,
       [30.510818, 30.51081 , 30.51081 , ..., 30.506065, 30.506023, 30.505974],
       [30.515388, 30.51538 , 30.51538 , ..., 30.510628, 30.510586, 30.510536],
       [30.519962, 30.51995 , 30.519936, ..., 30.515198, 30.51514 , 30.515106]],
      dtype=float32)
    • longitude
      (south_north, west_east)
      float32
      ...
      units :
      degrees_east
      standard_name :
      longitude
      FieldType :
      104
      MemoryOrder :
      XY
      description :
      LONGITUDE, WEST IS NEGATIVE
      stagger :
      array([[-94.90857 , -94.90332 , -94.89807 , ..., -93.88428 , -93.87903 ,
        -93.87378 ],
       [-94.90857 , -94.90332 , -94.89807 , ..., -93.88422 , -93.87897 ,
        -93.87372 ],
       [-94.90857 , -94.90332 , -94.89807 , ..., -93.884186, -93.87894 ,
        -93.87366 ],
       ...,
       [-94.907776, -94.902466, -94.897156, ..., -93.874176, -93.868866,
        -93.86359 ],
       [-94.907745, -94.902466, -94.897156, ..., -93.874115, -93.868805,
        -93.863525],
       [-94.907745, -94.902466, -94.897156, ..., -93.874054, -93.868774,
        -93.863464]], dtype=float32)
    • model_level_number
      ()
      int64
      ...
      bounds :
      model_level_number_bnds
      units :
      1
      standard_name :
      model_level_number
      array(39)
    • x
      (west_east)
      float64
      ...
      bounds :
      x_bnds
      units :
      m
      standard_name :
      projection_x_coordinate
      long_name :
      x
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    • y
      (south_north)
      float64
      ...
      bounds :
      y_bnds
      units :
      m
      standard_name :
      projection_y_coordinate
      long_name :
      y
      array([140750., 141250., 141750., 142250., 142750., 143250., 143750., 144250.,
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       156750., 157250., 157750., 158250., 158750., 159250., 159750., 160250.,
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       172750., 173250., 173750., 174250., 174750., 175250., 175750., 176250.,
       176750., 177250., 177750., 178250., 178750., 179250., 179750., 180250.,
       180750., 181250., 181750., 182250., 182750., 183250., 183750., 184250.,
       184750., 185250., 185750., 186250., 186750., 187250., 187750., 188250.,
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       232750., 233250., 233750., 234250., 234750., 235250., 235750., 236250.,
       236750., 237250., 237750., 238250., 238750., 239250.])
    • x_0
      (west_east)
      int64
      ...
      units :
      1
      long_name :
      x
      array([281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294,
       295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308,
       309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322,
       323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336,
       337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350,
       351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364,
       365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378,
       379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392,
       393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406,
       407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420,
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       463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476,
       477, 478])
    • y_0
      (south_north)
      int64
      ...
      units :
      1
      long_name :
      y
      array([281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294,
       295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308,
       309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322,
       323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336,
       337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350,
       351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364,
       365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378,
       379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392,
       393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406,
       407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420,
       421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434,
       435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448,
       449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462,
       463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476,
       477, 478])
  • long_name :
    w
    units :
    m s-1
    cell_methods :
    model_level_number: maximum
Show/Hide data repr Show/Hide attributes
xarray.DataArray
'twc'
  • time: 47
  • bottom_top: 94
  • south_north: 198
  • west_east: 198
  • ...
    [173203272 values with dtype=float32]
    • time
      (time)
      datetime64[ns]
      2013-06-19T20:05:00 ... 2013-06-19T23:55:00
      axis :
      T
      standard_name :
      time
      array(['2013-06-19T20:05:00.000000000', '2013-06-19T20:10:00.000000000',
       '2013-06-19T20:15:00.000000000', '2013-06-19T20:20:00.000000000',
       '2013-06-19T20:25:00.000000000', '2013-06-19T20:30:00.000000000',
       '2013-06-19T20:35:00.000000000', '2013-06-19T20:40:00.000000000',
       '2013-06-19T20:45:00.000000000', '2013-06-19T20:50:00.000000000',
       '2013-06-19T20:55:00.000000000', '2013-06-19T21:00:00.000000000',
       '2013-06-19T21:05:00.000000000', '2013-06-19T21:10:00.000000000',
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       '2013-06-19T21:45:00.000000000', '2013-06-19T21:50:00.000000000',
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       '2013-06-19T22:45:00.000000000', '2013-06-19T22:50:00.000000000',
       '2013-06-19T22:55:00.000000000', '2013-06-19T23:00:00.000000000',
       '2013-06-19T23:05:00.000000000', '2013-06-19T23:10:00.000000000',
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       '2013-06-19T23:45:00.000000000', '2013-06-19T23:50:00.000000000',
       '2013-06-19T23:55:00.000000000'], dtype='datetime64[ns]')
    • bottom_top
      (bottom_top)
      int64
      0 1 2 3 4 5 6 ... 88 89 90 91 92 93
      units :
      1
      long_name :
      bottom_top
      array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16, 17,
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       54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
       72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,
       90, 91, 92, 93])
    • south_north
      (south_north)
      int64
      281 282 283 284 ... 475 476 477 478
      units :
      1
      long_name :
      south_north
      array([281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294,
       295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308,
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       407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420,
       421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434,
       435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448,
       449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462,
       463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476,
       477, 478])
    • west_east
      (west_east)
      int64
      281 282 283 284 ... 475 476 477 478
      units :
      1
      long_name :
      west_east
      array([281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294,
       295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308,
       309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322,
       323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336,
       337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350,
       351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364,
       365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378,
       379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392,
       393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406,
       407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420,
       421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434,
       435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448,
       449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462,
       463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476,
       477, 478])
    • latitude
      (south_north, west_east)
      float32
      ...
      units :
      degrees_north
      standard_name :
      latitude
      FieldType :
      104
      MemoryOrder :
      XY
      description :
      LATITUDE, SOUTH IS NEGATIVE
      stagger :
      array([[29.62032 , 29.620296, 29.620296, ..., 29.615593, 29.615551, 29.615501],
       [29.624874, 29.624874, 29.624859, ..., 29.620167, 29.620113, 29.620071],
       [29.629444, 29.629429, 29.629429, ..., 29.624718, 29.624683, 29.624634],
       ...,
       [30.510818, 30.51081 , 30.51081 , ..., 30.506065, 30.506023, 30.505974],
       [30.515388, 30.51538 , 30.51538 , ..., 30.510628, 30.510586, 30.510536],
       [30.519962, 30.51995 , 30.519936, ..., 30.515198, 30.51514 , 30.515106]],
      dtype=float32)
    • longitude
      (south_north, west_east)
      float32
      ...
      units :
      degrees_east
      standard_name :
      longitude
      FieldType :
      104
      MemoryOrder :
      XY
      description :
      LONGITUDE, WEST IS NEGATIVE
      stagger :
      array([[-94.90857 , -94.90332 , -94.89807 , ..., -93.88428 , -93.87903 ,
        -93.87378 ],
       [-94.90857 , -94.90332 , -94.89807 , ..., -93.88422 , -93.87897 ,
        -93.87372 ],
       [-94.90857 , -94.90332 , -94.89807 , ..., -93.884186, -93.87894 ,
        -93.87366 ],
       ...,
       [-94.907776, -94.902466, -94.897156, ..., -93.874176, -93.868866,
        -93.86359 ],
       [-94.907745, -94.902466, -94.897156, ..., -93.874115, -93.868805,
        -93.863525],
       [-94.907745, -94.902466, -94.897156, ..., -93.874054, -93.868774,
        -93.863464]], dtype=float32)
    • model_level_number
      (bottom_top)
      int64
      ...
      units :
      1
      standard_name :
      model_level_number
      array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16, 17,
       18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
       36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
       54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
       72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,
       90, 91, 92, 93])
    • x
      (west_east)
      float64
      ...
      bounds :
      x_bnds
      units :
      m
      standard_name :
      projection_x_coordinate
      long_name :
      x
      array([140750., 141250., 141750., 142250., 142750., 143250., 143750., 144250.,
       144750., 145250., 145750., 146250., 146750., 147250., 147750., 148250.,
       148750., 149250., 149750., 150250., 150750., 151250., 151750., 152250.,
       152750., 153250., 153750., 154250., 154750., 155250., 155750., 156250.,
       156750., 157250., 157750., 158250., 158750., 159250., 159750., 160250.,
       160750., 161250., 161750., 162250., 162750., 163250., 163750., 164250.,
       164750., 165250., 165750., 166250., 166750., 167250., 167750., 168250.,
       168750., 169250., 169750., 170250., 170750., 171250., 171750., 172250.,
       172750., 173250., 173750., 174250., 174750., 175250., 175750., 176250.,
       176750., 177250., 177750., 178250., 178750., 179250., 179750., 180250.,
       180750., 181250., 181750., 182250., 182750., 183250., 183750., 184250.,
       184750., 185250., 185750., 186250., 186750., 187250., 187750., 188250.,
       188750., 189250., 189750., 190250., 190750., 191250., 191750., 192250.,
       192750., 193250., 193750., 194250., 194750., 195250., 195750., 196250.,
       196750., 197250., 197750., 198250., 198750., 199250., 199750., 200250.,
       200750., 201250., 201750., 202250., 202750., 203250., 203750., 204250.,
       204750., 205250., 205750., 206250., 206750., 207250., 207750., 208250.,
       208750., 209250., 209750., 210250., 210750., 211250., 211750., 212250.,
       212750., 213250., 213750., 214250., 214750., 215250., 215750., 216250.,
       216750., 217250., 217750., 218250., 218750., 219250., 219750., 220250.,
       220750., 221250., 221750., 222250., 222750., 223250., 223750., 224250.,
       224750., 225250., 225750., 226250., 226750., 227250., 227750., 228250.,
       228750., 229250., 229750., 230250., 230750., 231250., 231750., 232250.,
       232750., 233250., 233750., 234250., 234750., 235250., 235750., 236250.,
       236750., 237250., 237750., 238250., 238750., 239250.])
    • y
      (south_north)
      float64
      ...
      bounds :
      y_bnds
      units :
      m
      standard_name :
      projection_y_coordinate
      long_name :
      y
      array([140750., 141250., 141750., 142250., 142750., 143250., 143750., 144250.,
       144750., 145250., 145750., 146250., 146750., 147250., 147750., 148250.,
       148750., 149250., 149750., 150250., 150750., 151250., 151750., 152250.,
       152750., 153250., 153750., 154250., 154750., 155250., 155750., 156250.,
       156750., 157250., 157750., 158250., 158750., 159250., 159750., 160250.,
       160750., 161250., 161750., 162250., 162750., 163250., 163750., 164250.,
       164750., 165250., 165750., 166250., 166750., 167250., 167750., 168250.,
       168750., 169250., 169750., 170250., 170750., 171250., 171750., 172250.,
       172750., 173250., 173750., 174250., 174750., 175250., 175750., 176250.,
       176750., 177250., 177750., 178250., 178750., 179250., 179750., 180250.,
       180750., 181250., 181750., 182250., 182750., 183250., 183750., 184250.,
       184750., 185250., 185750., 186250., 186750., 187250., 187750., 188250.,
       188750., 189250., 189750., 190250., 190750., 191250., 191750., 192250.,
       192750., 193250., 193750., 194250., 194750., 195250., 195750., 196250.,
       196750., 197250., 197750., 198250., 198750., 199250., 199750., 200250.,
       200750., 201250., 201750., 202250., 202750., 203250., 203750., 204250.,
       204750., 205250., 205750., 206250., 206750., 207250., 207750., 208250.,
       208750., 209250., 209750., 210250., 210750., 211250., 211750., 212250.,
       212750., 213250., 213750., 214250., 214750., 215250., 215750., 216250.,
       216750., 217250., 217750., 218250., 218750., 219250., 219750., 220250.,
       220750., 221250., 221750., 222250., 222750., 223250., 223750., 224250.,
       224750., 225250., 225750., 226250., 226750., 227250., 227750., 228250.,
       228750., 229250., 229750., 230250., 230750., 231250., 231750., 232250.,
       232750., 233250., 233750., 234250., 234750., 235250., 235750., 236250.,
       236750., 237250., 237750., 238250., 238750., 239250.])
    • x_0
      (west_east)
      int64
      ...
      units :
      1
      long_name :
      x
      array([281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294,
       295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308,
       309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322,
       323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336,
       337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350,
       351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364,
       365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378,
       379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392,
       393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406,
       407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420,
       421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434,
       435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448,
       449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462,
       463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476,
       477, 478])
    • y_0
      (south_north)
      int64
      ...
      units :
      1
      long_name :
      y
      array([281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294,
       295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308,
       309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322,
       323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336,
       337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350,
       351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364,
       365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378,
       379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392,
       393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406,
       407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420,
       421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434,
       435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448,
       449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462,
       463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476,
       477, 478])
  • long_name :
    TWC
    units :
    kg kg-1
[10]:

#Set up directory to save output and plots:
savedir='Save'
if not os.path.exists(savedir):
    os.makedirs(savedir)
plot_dir="Plot"
if not os.path.exists(plot_dir):
    os.makedirs(plot_dir)

Feature detection:

Perform feature detection based on midlevel maximum vertical velocity and a range of threshold values.

[11]:

# Determine temporal and spatial sampling of the input data:
dxy,dt=tobac.utils.get_spacings(W_mid_max)

[12]:

# Keyword arguments for feature detection step:
parameters_features={}
parameters_features['position_threshold']='weighted_diff'
parameters_features['sigma_threshold']=0.5
parameters_features['min_num']=3
parameters_features['min_distance']=0
parameters_features['sigma_threshold']=1
parameters_features['threshold']=[3,5,10] #m/s
parameters_features['n_erosion_threshold']=0
parameters_features['n_min_threshold']=3

[13]:

# Perform feature detection and save results:
print('start feature detection based on midlevel column maximum vertical velocity')
dxy,dt=tobac.utils.get_spacings(W_mid_max)
Features=tobac.themes.tobac_v1.feature_detection_multithreshold(W_mid_max,dxy,**parameters_features)
print('feature detection performed start saving features')
Features.to_netcdf(os.path.join(savedir,'Features.nc'))
print('features saved')

start feature detection based on midlevel column maximum vertical velocity
     frame  idx      hdim_1      hdim_2  num  threshold_value  feature  \
0        0    3   86.765659   53.350266   10                3        1
1        0    6  109.581883   65.230958    7                3        2
2        0    8  116.808699  191.185786    6                3        3
3        0   12  155.613171   33.200565    5                3        4
4        0   14   84.857363   37.092481   43                5        5
..     ...  ...         ...         ...  ...              ...      ...
624     46   36  144.848990  116.270462   51               10      625
625     46   38  158.442623  106.995282    6               10      626
626     46   39  172.189120    3.980561   53               10      627
627     46   40  186.763110  101.952079   17               10      628
628     46   41  190.393192  179.765727    4               10      629

                    time              timestr  south_north   west_east  \
0    2013-06-19 20:05:00  2013-06-19 20:05:00   367.765659  334.350266
1    2013-06-19 20:05:00  2013-06-19 20:05:00   390.581883  346.230958
2    2013-06-19 20:05:00  2013-06-19 20:05:00   397.808699  472.185786
3    2013-06-19 20:05:00  2013-06-19 20:05:00   436.613171  314.200565
4    2013-06-19 20:05:00  2013-06-19 20:05:00   365.857363  318.092481
..                   ...                  ...          ...         ...
624  2013-06-19 23:55:00  2013-06-19 23:55:00   425.848990  397.270462
625  2013-06-19 23:55:00  2013-06-19 23:55:00   439.442623  387.995282
626  2013-06-19 23:55:00  2013-06-19 23:55:00   453.189120  284.980561
627  2013-06-19 23:55:00  2013-06-19 23:55:00   467.763110  382.952079
628  2013-06-19 23:55:00  2013-06-19 23:55:00   471.393192  460.765727

     bottom_top_stag  model_level_number  projection_y_coordinate           y  \
0         334.350266          334.350266            184132.829257  367.765659
1         346.230958          346.230958            195540.941390  390.581883
2         472.185786          472.185786            199154.349360  397.808699
3         314.200565          314.200565            218556.585318  436.613171
4         318.092481          318.092481            183178.681637  365.857363
..               ...                 ...                      ...         ...
624       397.270462          397.270462            213174.494771  425.848990
625       387.995282          387.995282            219971.311750  439.442623
626       284.980561          284.980561            226844.559837  453.189120
627       382.952079          382.952079            234131.555024  467.763110
628       460.765727          460.765727            235946.595843  471.393192

                 latitude             longitude  projection_x_coordinate  \
0    [30.016038859108175]  [-94.62685053589469]            167425.132894
1    [30.120045475411185]   [-94.5637249988283]            173365.479208
2     [30.14916169399921]  [-93.89838383702785]            236342.893153
3     [30.33071080683231]  [-94.73227239126004]            157350.282423
4    [30.007544572713726]  [-94.71261994128162]            159296.240490
..                    ...                   ...                      ...
624  [30.279932206676968]  [-94.29310184128425]            198885.230853
625  [30.342259128747088]  [-94.34174723855492]            194247.641224
626   [30.40663218356964]  [-94.88678519978228]            142740.280723
627  [30.471714442853838]  [-94.36760066497843]            191726.039457
628  [30.485679966689368]  [-93.95513846172912]            230632.863513

              x
0    334.350266
1    346.230958
2    472.185786
3    314.200565
4    318.092481
..          ...
624  397.270462
625  387.995282
626  284.980561
627  382.952079
628  460.765727

[629 rows x 19 columns]
['time', 'south_north', 'west_east', 'bottom_top_stag', 'latitude', 'longitude', 'model_level_number', 'x', 'y', 'x_0', 'y_0']
feature detection performed start saving features
features saved
Segmentation:
Perform segmentation based on 3D total condensate field to determine cloud volumes associated to identified features:
[14]:

parameters_segmentation_TWC={}
parameters_segmentation_TWC['method']='watershed'
parameters_segmentation_TWC['threshold']=0.1e-3  # kg/kg mixing ratio

[15]:

print('Start segmentation based on total water content')
Mask_TWC,Features_TWC=tobac.themes.tobac_v1.segmentation(Features,TWC,dxy,**parameters_segmentation_TWC)
print('segmentation TWC performed, start saving results to files')
Mask_TWC.to_netcdf(os.path.join(savedir,'Mask_Segmentation_TWC.nc'))
Features_TWC.to_netcdf(os.path.join(savedir,'Features_TWC.nc'))
print('segmentation TWC performed and saved')

Start segmentation based on total water content
<xarray.DataArray 'twc' (time: 47, bottom_top: 94, south_north: 198, west_east: 198)>
[173203272 values with dtype=float32]
Coordinates:
  * time                (time) datetime64[ns] 2013-06-19T20:05:00 ... 2013-06-19T23:55:00
  * bottom_top          (bottom_top) int64 0 1 2 3 4 5 6 ... 88 89 90 91 92 93
  * south_north         (south_north) int64 281 282 283 284 ... 475 476 477 478
  * west_east           (west_east) int64 281 282 283 284 ... 475 476 477 478
    latitude            (south_north, west_east) float32 29.62032 ... 30.515106
    longitude           (south_north, west_east) float32 -94.90857 ... -93.863464
    model_level_number  (bottom_top) int64 0 1 2 3 4 5 6 ... 88 89 90 91 92 93
    x                   (west_east) float64 1.408e+05 1.412e+05 ... 2.392e+05
    y                   (south_north) float64 1.408e+05 1.412e+05 ... 2.392e+05
    x_0                 (west_east) int64 281 282 283 284 ... 475 476 477 478
    y_0                 (south_north) int64 281 282 283 284 ... 475 476 477 478
Attributes:
    long_name:  TWC
    units:      kg kg-1

/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,
/home/senf/TROPOS/tmp/tobac-dev-2020-07-09/test-env/lib/python3.7/site-packages/skimage/morphology/_deprecated.py:5: skimage_deprecation: Function ``watershed`` is deprecated and will be removed in version 0.19. Use ``skimage.segmentation.watershed`` instead.
  def watershed(image, markers=None, connectivity=1, offset=None, mask=None,

segmentation TWC performed, start saving results to files
segmentation TWC performed and saved
Trajectory linking:
Detected features are linked into cloud trajectories using the trackpy library (http://soft-matter.github.io/trackpy). This takes the feature positions determined in the feature detection step into account but does not include information on the shape of the identified objects.
[16]:

# Keyword arguments for linking step:
parameters_linking={}
parameters_linking['method_linking']='predict'
parameters_linking['adaptive_stop']=0.2
parameters_linking['adaptive_step']=0.95
parameters_linking['extrapolate']=0
parameters_linking['order']=1
parameters_linking['subnetwork_size']=100
parameters_linking['memory']=0
parameters_linking['time_cell_min']=5*60
parameters_linking['method_linking']='predict'
parameters_linking['v_max']=10
parameters_linking['d_min']=2000

[17]:

# Perform linking and save results:
Track=tobac.themes.tobac_v1.linking_trackpy(Features,W_mid_max,dt=dt,dxy=dxy,**parameters_linking)
Track.to_netcdf(os.path.join(savedir,'Track.nc'))

Frame 46: 18 trajectories present.

Visualisation:

[18]:

# Set extent for maps plotted in the following cells ( in the form [lon_min,lon_max,lat_min,lat_max])
axis_extent=[-95,-93.8,29.5,30.6]

[19]:

# Plot map with all individual tracks:
import cartopy.crs as ccrs
fig_map,ax_map=plt.subplots(figsize=(10,10),subplot_kw={'projection': ccrs.PlateCarree()})
ax_map=tobac.plot.map_tracks(Track,axis_extent=axis_extent,axes=ax_map)

[21]:

# Create animation showing tracked cells with outline of cloud volumes and the midlevel vertical velocity as a background field:
animation_tobac=tobac.plot.animation_mask_field(Track,Features,W_mid_max,Mask_TWC,
                                          axis_extent=axis_extent,#figsize=figsize,orientation_colorbar='horizontal',pad_colorbar=0.2,
                                          vmin=0,vmax=20,extend='both',cmap='Blues',
                                          interval=500,figsize=(10,7),
                                          plot_outline=True,plot_marker=True,marker_track='x',plot_number=True,plot_features=True)

[22]:

# Display animation:
from IPython.display import HTML, Image, display
HTML(animation_tobac.to_html5_video())

[22]:

[23]:

# # Save animation to file
# savefile_animation=os.path.join(plot_dir,'Animation.mp4')
# animation_tobac.save(savefile_animation,dpi=200)
# print(f'animation saved to {savefile_animation}')

[24]:

# Updraft lifetimes of tracked cells:
fig_lifetime,ax_lifetime=plt.subplots()
tobac.plot.plot_lifetime_histogram_bar(Track,axes=ax_lifetime,bin_edges=np.arange(0,120,10),density=False,width_bar=8)
ax_lifetime.set_xlabel('lifetime (min)')
ax_lifetime.set_ylabel('counts')

[24]:

Text(0, 0.5, 'counts')