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adelepoulle
committed
move action in class method
1 parent 4215eac commit 7974898

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-255
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3 files changed

+351
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‎src/py_eddy_tracker/observations.py‎

Lines changed: 14 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@
2828
===========================================================================
2929
3030
"""
31-
from numpy import zeros, empty, nan, arange, interp, where
31+
from numpy import zeros, empty, nan, arange, interp, where, unique
3232
from netCDF4 import Dataset
3333
from py_eddy_tracker.tools import distance_matrix
3434
from . import VAR_DESCR, VAR_DESCR_inv
@@ -78,6 +78,11 @@ def __init__(self, size=0, track_extra_variables=False):
7878
def __repr__(self):
7979
return str(self.observations)
8080

81+
def __getitem__(self, attr):
82+
if attr in self.elements:
83+
return self.observations[attr]
84+
raise KeyError('%s unknown' % attr)
85+
8186
@property
8287
def dtype(self):
8388
dtype = list()
@@ -192,7 +197,7 @@ def tracking(self, other):
192197
dist = self.distance(other)
193198
i_self, i_other = where(dist < 20.)
194199

195-
logging.debug('%d match with previous', i_self.shape[0])
200+
logging.debug('%d matched with previous', i_self.shape[0])
196201
return i_self, i_other
197202

198203

@@ -222,14 +227,20 @@ def filled_by_interpolation(self, mask):
222227
self.obs[var][mask] = interp(index[mask], index[-mask],
223228
self.obs[var][-mask])
224229

225-
def extract_longer_eddies(self, nb_min, nb_obs):
230+
def extract_longer_eddies(self, nb_min, nb_obs, compress_id=True):
226231
m = nb_obs >= nb_min
227232
nb_obs_select = m.sum()
228233
logging.info('Selection of %d observations', nb_obs_select)
229234
eddies = TrackEddiesObservations(size=nb_obs_select)
230235
eddies.sign_type = self.sign_type
231236
for var, _ in eddies.obs.dtype.descr:
232237
eddies.obs[var] = self.obs[var][m]
238+
if compress_id:
239+
list_id = unique(eddies.obs['track'])
240+
list_id.sort()
241+
id_translate = arange(list_id.max() + 1)
242+
id_translate[list_id] = arange(len(list_id)) + 1
243+
eddies.obs['track'] = id_translate[eddies.obs['track']]
233244
return eddies
234245

235246
@property

‎src/py_eddy_tracker/tracking.py‎

Lines changed: 323 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,323 @@
1+
# -*- coding: utf-8 -*-
2+
"""
3+
===========================================================================
4+
This file is part of py-eddy-tracker.
5+
6+
py-eddy-tracker is free software: you can redistribute it and/or modify
7+
it under the terms of the GNU General Public License as published by
8+
the Free Software Foundation, either version 3 of the License, or
9+
(at your option) any later version.
10+
11+
py-eddy-tracker is distributed in the hope that it will be useful,
12+
but WITHOUT ANY WARRANTY; without even the implied warranty of
13+
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14+
GNU General Public License for more details.
15+
16+
You should have received a copy of the GNU General Public License
17+
along with py-eddy-tracker. If not, see <http://www.gnu.org/licenses/>.
18+
19+
Copyright (c) 2014-2015 by Evan Mason
20+
Email: [email protected]
21+
===========================================================================
22+
23+
24+
py_eddy_tracker_amplitude.py
25+
26+
Version 2.0.3
27+
28+
===========================================================================
29+
30+
"""
31+
from py_eddy_tracker.observations import EddiesObservations, \
32+
VirtualEddiesObservations, TrackEddiesObservations
33+
from numpy import bool_, array, arange, ones, setdiff1d, zeros, uint16
34+
import logging
35+
36+
37+
class Correspondances(list):
38+
"""Object to store correspondances
39+
And run tracking
40+
"""
41+
UINT32_MAX = 4294967295
42+
# Prolongation limit to 255
43+
VIRTUAL_DTYPE = 'u1'
44+
# ID limit to 4294967295
45+
ID_DTYPE = 'u4'
46+
# Track limit to 65535
47+
N_DTYPE = 'u2'
48+
49+
50+
def __init__(self, datasets, virtual=0):
51+
"""Initiate tracking
52+
"""
53+
# Correspondance dtype
54+
self.correspondance_dtype = [('in', 'u2'),
55+
('out', 'u2'),
56+
('id', self.ID_DTYPE)]
57+
# To count ID
58+
self.current_id = 0
59+
# Dataset to iterate
60+
self.datasets = datasets
61+
self.previous2_obs = None
62+
self.previous_obs = None
63+
self.current_obs = EddiesObservations.load_from_netcdf(
64+
self.datasets[0])
65+
66+
# To use virtual obs
67+
# Number of obs which can prolongate real observations
68+
self.nb_virtual = virtual
69+
# Activation or not
70+
self.virtual = virtual > 0
71+
self.virtual_obs = None
72+
self.previous_virtual_obs = None
73+
if self.virtual:
74+
# Add field to dtype to follow virtual observations
75+
self.correspondance_dtype += [
76+
('virtual', bool_),
77+
('virtual_length', self.VIRTUAL_DTYPE)]
78+
79+
# Array to simply merged
80+
self.nb_obs_by_tracks = None
81+
self.i_current_by_tracks = None
82+
self.nb_obs = 0
83+
self.eddies = None
84+
85+
def swap_dataset(self, dataset):
86+
"""
87+
"""
88+
self.previous2_obs = self.previous_obs
89+
self.previous_obs = self.current_obs
90+
self.current_obs = EddiesObservations.load_from_netcdf(dataset)
91+
92+
def store_correspondance(self, i_previous, i_current):
93+
correspondance = array(
94+
i_previous,
95+
dtype=self.correspondance_dtype)
96+
correspondance['out'] = i_current
97+
98+
if self.virtual:
99+
correspondance['virtual'] = i_previous >= nb_real_obs
100+
101+
def id_generator(self, nb_id):
102+
"""Generation id and incrementation
103+
"""
104+
values = arange(self.current_id, self.current_id + nb_id)
105+
self.current_id += nb_id
106+
return values
107+
108+
def recense_dead_id_to_extend(self):
109+
"""Recense dead id to extend in virtual observation
110+
"""
111+
nb_virtual_extend = 0
112+
# List previous id which are not use in the next step
113+
dead_id = setdiff1d(self[-2]['id'], self[-1]['id'])
114+
nb_dead = dead_id.shape[0]
115+
logging.debug('%d death of real obs in this step', nb_dead)
116+
if not self.virtual:
117+
return
118+
# Creation of an virtual step for dead one
119+
self.virtual_obs = VirtualEddiesObservations(size=nb_dead + nb_virtual_extend)
120+
121+
# Find mask/index on previous correspondance to extrapolate
122+
# position
123+
list_previous_id = self[-2]['id'].tolist()
124+
i_dead_id = [list_previous_id.index(i) for i in dead_id]
125+
126+
# Selection of observations on N-2 and N-1
127+
obs_a = self.previous2_obs.obs[self[-2][i_dead_id]['in']]
128+
obs_b = self.previous_obs.obs[self[-2][i_dead_id]['out']]
129+
# Position N-2 : A
130+
# Position N-1 : B
131+
# Virtual Position : C
132+
# New position C = B + AB
133+
self.virtual_obs['dlon'][:nb_dead] = obs_b['lon'] - obs_a['lon']
134+
self.virtual_obs['dlat'][:nb_dead] = obs_b['lat'] - obs_a['lat']
135+
self.virtual_obs['lon'][:nb_dead
136+
] = obs_b['lon'] + self.virtual_obs['dlon'][:nb_dead]
137+
self.virtual_obs['lat'][:nb_dead
138+
] = obs_b['lat'] + self.virtual_obs['dlat'][:nb_dead]
139+
# Id which are extended
140+
self.virtual_obs['track'][:nb_dead] = dead_id
141+
# Add previous virtual
142+
if nb_virtual_extend > 0:
143+
obs_to_extend = self.previous_virtual_obs.obs[i_virtual_dead_id][alive_virtual_obs]
144+
self.virtual_obs['lon'][nb_dead:] = obs_to_extend['lon'] + obs_to_extend['dlon']
145+
self.virtual_obs['lat'][nb_dead:] = obs_to_extend['lat'] + obs_to_extend['dlat']
146+
self.virtual_obs['track'][nb_dead:] = obs_to_extend['track']
147+
self.virtual_obs['segment_size'][nb_dead:] = obs_to_extend['segment_size']
148+
# Count
149+
self.virtual_obs['segment_size'][:] += 1
150+
151+
def track(self):
152+
"""Run tracking
153+
"""
154+
START = True
155+
FLG_VIRTUAL = False
156+
# We begin with second file, first one is in previous
157+
for file_name in self.datasets[1:]:
158+
self.swap_dataset(file_name)
159+
logging.debug('%s match with previous state', file_name)
160+
logging.debug('%d obs to match', len(self.current_obs))
161+
162+
nb_real_obs = len(self.previous_obs)
163+
if FLG_VIRTUAL:
164+
logging.debug('%d virtual obs will be add to previous',
165+
len(self.virtual_obs))
166+
# If you comment this the virtual fonctionnality will be disable
167+
self.previous_obs = self.previous_obs.merge(self.virtual_obs)
168+
169+
i_previous, i_current = self.previous_obs.tracking(self.current_obs)
170+
nb_match = i_previous.shape[0]
171+
172+
#~ self.store_correspondance(i_previous, i_current)
173+
correspondance = array(i_previous, dtype=self.correspondance_dtype)
174+
correspondance['out'] = i_current
175+
176+
if self.virtual:
177+
correspondance['virtual'] = i_previous >= nb_real_obs
178+
179+
if START:
180+
START = False
181+
# Set an id for each match
182+
correspondance['id'] = self.id_generator(nb_match)
183+
self.append(correspondance)
184+
continue
185+
186+
# We set all id to UINT32_MAX
187+
id_previous = ones(len(self.previous_obs), dtype=self.ID_DTYPE) * self.UINT32_MAX
188+
# We get old id for previously eddies tracked
189+
previous_id = self[-1]['id']
190+
id_previous[self[-1]['out']] = previous_id
191+
correspondance['id'] = id_previous[correspondance['in']]
192+
193+
if FLG_VIRTUAL:
194+
nb_rebirth = correspondance['virtual'].sum()
195+
if nb_rebirth != 0:
196+
logging.debug('%d re-birth due to prolongation with'
197+
' virtual observations', nb_rebirth)
198+
# Set id for virtual
199+
i_virtual = correspondance['in'][correspondance['virtual']] - nb_real_obs
200+
correspondance['id'][correspondance['virtual']] = \
201+
self.virtual_obs['track'][i_virtual]
202+
correspondance['virtual_length'][correspondance['virtual']] = \
203+
self.virtual_obs['segment_size'][i_virtual]
204+
205+
# new_id is equal to UINT32_MAX we must add a new ones
206+
# we count the number of new
207+
mask_new_id = correspondance['id'] == UINT32_MAX
208+
nb_new_tracks = mask_new_id.sum()
209+
logging.debug('%d birth in this step', nb_new_tracks)
210+
# Set new id
211+
correspondance['id'][mask_new_id] = self.id_generator(nb_new_tracks)
212+
213+
self.append(correspondance)
214+
215+
# SECTION for virtual observation
216+
nb_virtual_prolongate = 0
217+
if FLG_VIRTUAL:
218+
# Save previous state to count virtual obs
219+
self.previous_virtual_obs = self.virtual_obs
220+
virtual_dead_id = setdiff1d(self.virtual_obs['track'],
221+
correspondance['id'])
222+
list_previous_virtual_id = self.virtual_obs['track'].tolist()
223+
i_virtual_dead_id = [
224+
list_previous_virtual_id.index(i) for i in virtual_dead_id]
225+
# Virtual obs which can be prolongate
226+
alive_virtual_obs = self.virtual_obs['segment_size'][i_virtual_dead_id] < self.nb_virtual
227+
nb_virtual_prolongate = alive_virtual_obs.sum()
228+
logging.debug('%d virtual obs will be prolongate on the '
229+
'next step', nb_virtual_prolongate)
230+
231+
self.recense_dead_id_to_extend()
232+
233+
if self.virtual:
234+
FLG_VIRTUAL = True
235+
236+
def prepare_merging(self):
237+
# count obs by tracks (we add directly one, because correspondance
238+
# is an interval)
239+
self.nb_obs_by_tracks = zeros(self.current_id, dtype=self.N_DTYPE) + 1
240+
for correspondance in self:
241+
self.nb_obs_by_tracks[correspondance['id']] += 1
242+
if self.virtual:
243+
# When start is virtual, we don't have a previous correspondance
244+
self.nb_obs_by_tracks[correspondance['id'][correspondance['virtual']]
245+
] += correspondance['virtual_length'][correspondance['virtual']]
246+
247+
# Compute index of each tracks
248+
self.i_current_by_tracks = self.nb_obs_by_tracks.cumsum() - self.nb_obs_by_tracks
249+
# Number of global obs
250+
self.nb_obs = nb_obs_by_tracks.sum()
251+
logging.info('%d tracks identified', self.current_id)
252+
logging.info('%d observations will be join', self.nb_obs)
253+
254+
def merge(self):
255+
# Start create netcdf to agglomerate all eddy
256+
self.eddies = TrackEddiesObservations(size=self.nb_obs)
257+
258+
# Calculate the index in each tracks, we compute in u4 and translate
259+
# in u2 (which are limited to 65535)
260+
logging.debug('Compute global index array (N)')
261+
n = arange(nb_obs,
262+
dtype='u4') - self.i_current_by_tracks.repeat(self.nb_obs_by_tracks)
263+
self.eddies['n'][:] = uint16(n)
264+
logging.debug('Compute global track array')
265+
self.eddies['track'][:] = arange(self.current_id).repeat(self.nb_obs_by_tracks)
266+
267+
# Start loading identification again to save in the finals tracks
268+
# Load first file
269+
eddies_previous = EddiesObservations.load_from_netcdf(self.datasets[0])
270+
# Set type of eddy with first file
271+
self.eddies.sign_type = eddies_previous.sign_type
272+
273+
# To know if the track start
274+
first_obs_save_in_tracks = zeros(i_current_by_tracks.shape,
275+
dtype=bool_)
276+
277+
for i, file_name in enumerate(FILENAMES[1:]):
278+
# Load current file (we begin with second one)
279+
self.current_obs = EddiesObservations.load_from_netcdf(file_name)
280+
# We select the list of id which are involve in the correspondance
281+
i_id = self[i]['id']
282+
# Index where we will write in the final object
283+
index_final = i_current_by_tracks[i_id]
284+
285+
# First obs of eddies
286+
m_first_obs = -first_obs_save_in_tracks[i_id]
287+
if m_first_obs.any():
288+
# Index in the current file
289+
index_in = self[i]['in'][m_first_obs]
290+
# Copy all variable
291+
for var, _ in eddies_current.obs.dtype.descr:
292+
self.eddies[var][index_final[m_first_obs]
293+
] = eddies_previous[var][index_in]
294+
# Increment
295+
i_current_by_tracks[i_id[m_first_obs]] += 1
296+
# Active this flag, we have only one first by tracks
297+
first_obs_save_in_tracks[i_id] = True
298+
index_final = i_current_by_tracks[i_id]
299+
300+
# Index in the current file
301+
index_current = self[i]['out']
302+
303+
if self.virtual:
304+
# If the flag virtual in correspondance is active,
305+
# the previous is virtual
306+
m_virtual = self[i]['virtual']
307+
if m_virtual.any():
308+
index_virtual = index_final[m_virtual]
309+
# Incrementing index
310+
i_current_by_tracks[i_id[m_virtual]
311+
] += self[i]['virtual_length'][m_virtual]
312+
# Get new index
313+
index_final = i_current_by_tracks[i_id]
314+
315+
# Copy all variable
316+
for var, _ in eddies_current.obs.dtype.descr:
317+
self.eddies[var][index_final
318+
] = eddies_current[var][index_current]
319+
320+
# Add increment for each index used
321+
i_current_by_tracks[i_id] += 1
322+
eddies_previous = eddies_current
323+

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