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jbdurandjbdurand
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Merge branch '1-release-2025' of github.com:openalea/sequence_analysis into 1-release-2025
2 parents ab82a8a + 57c0932 commit 04ec7fc

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Lines changed: 189 additions & 91 deletions

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‎.readthedocs.yml‎

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version: 2
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build:
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os: "ubuntu-24.04"
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tools:
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python: "mambaforge-22.9"
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conda:
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environment: conda/environment.yml
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sphinx:
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# Path to your Sphinx configuration file.
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configuration: doc/conf.py

‎conda/environment.yml‎

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name: sequence_analysis_dev
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channels:
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- conda-forge
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- openalea3/label/dev
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- openalea3
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dependencies:
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- python
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- pip
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- boost
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- matplotlib-base
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- openalea.stat_tool
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- compilers
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- pip:
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- -e '..[test,dev,doc]'
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‎conda/meta.yaml‎

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@@ -33,13 +33,13 @@ requirements:
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{% for dep in build_deps %}
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- {{ dep }}
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{% endfor %}
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- cmake
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- make # [not win]
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- openalea.stat_tool
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- boost
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build:
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- {{ compiler("cxx") }}
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- cmake
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- make # [not win]
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run:
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- python

‎doc/pyplots/example_oak_2.py‎

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#
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#########################################################################
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"""
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__revision__ = "$Id: test_exploratory.py 8676 2010-04-20 15:28:46Z cokelaer $"
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from os.path import join as pj
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from openalea.sequence_analysis import *
20-
from openalea.sequence_analysis.estimate import Estimate
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from openalea.sequence_analysis import get_shared_data as path
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from os.path import join as pj
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seq0 = Sequences(pj(path ,"chene_sessile_15pa.seq"))
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25+
seq0 = Sequences(pj(path("chene_sessile_15pa.seq")))
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# change of unit for the variable diameter of the annual shoot
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marginal3 = ExtractHistogram(seq0, "Value", 3)
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Plot(Cluster(marginal3, "Information", 0.75))
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#Plot(Cluster(marginal3, "Information", 0.61))
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#Plot(Cluster(marginal3, "Step", 10))
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# Plot(Cluster(marginal3, "Information", 0.61))
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# Plot(Cluster(marginal3, "Step", 10))

‎doc/pyplots/example_oak_4.py‎

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@@ -14,27 +14,27 @@
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#
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#########################################################################
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"""
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__revision__ = "$Id: test_exploratory.py 8676 2010-04-20 15:28:46Z cokelaer $"
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from openalea.sequence_analysis import *
20-
from openalea.sequence_analysis.estimate import Estimate
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from openalea.sequence_analysis import get_shared_data as path
22-
from os.path import join as pj
23-
seq0 = Sequences(pj(path ,"chene_sessile_15pa.seq"))
24-
#Plot(seq0, ViewPoint="Data")
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seq0 = Sequences(path("chene_sessile_15pa.seq"))
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# Plot(seq0, ViewPoint="Data")
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# change of unit for the variable diameter of the annual shoot
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marginal3 = ExtractHistogram(seq0, "Value", 3)
30-
#Plot(Cluster(marginal3, "Information", 0.75))
31-
#Plot(Cluster(marginal3, "Information", 0.61))
32-
#Plot(Cluster(marginal3, "Step", 10))
30+
# Plot(Cluster(marginal3, "Information", 0.75))
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# Plot(Cluster(marginal3, "Information", 0.61))
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# Plot(Cluster(marginal3, "Step", 10))
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vec10 = Vectors(seq0)
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# plot of the average sequence
37-
#Plot(Regression(vec10, "MovingAverage", 1, 2, [1]))
37+
# Plot(Regression(vec10, "MovingAverage", 1, 2, [1]))
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3939
vec95 = ValueSelect(vec10, 1, 95)
4040
vec96 = ValueSelect(vec10, 1, 96)
@@ -43,10 +43,12 @@
4343
VarianceAnalysis(vec10, 1, 2, "N")
4444

4545

46-
#print type(ExtractHistogram(vec95, 2))
46+
# print type(ExtractHistogram(vec95, 2))
4747

48-
Compare(ExtractHistogram(vec95, 2), ExtractHistogram(vec96, 2), ExtractHistogram(vec97, 2), "N")
48+
Compare(
49+
ExtractHistogram(vec95, 2),
50+
ExtractHistogram(vec96, 2),
51+
ExtractHistogram(vec97, 2),
52+
"N",
53+
)
4954
Plot(ExtractHistogram(vec95, 2), ExtractHistogram(vec96, 2), ExtractHistogram(vec97, 2))
50-
51-
52-

‎doc/pyplots/example_oak_5.py‎

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Original file line numberDiff line numberDiff line change
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#
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#########################################################################
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"""
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__revision__ = "$Id: test_exploratory.py 8676 2010-04-20 15:28:46Z cokelaer $"
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20+
import os.path.join as pj
21+
1922
from openalea.sequence_analysis import *
20-
from openalea.sequence_analysis.estimate import Estimate
2123
from openalea.sequence_analysis import get_shared_data as path
22-
from os.path import join as pj
23-
seq0 = Sequences(pj(path ,"chene_sessile_15pa.seq"))
24-
#Plot(seq0, ViewPoint="Data")
24+
25+
seq0 = Sequences(pj(path("chene_sessile_15pa.seq")))
26+
# Plot(seq0, ViewPoint="Data")
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2628

2729
# change of unit for the variable diameter of the annual shoot
@@ -34,7 +36,7 @@
3436
vec10 = Vectors(seq0)
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3638
# plot of the average sequence
37-
#Plot(Regression(vec10, "MovingAverage", 1, 2, [1]))
39+
# Plot(Regression(vec10, "MovingAverage", 1, 2, [1]))
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3941
vec95 = ValueSelect(vec10, 1, 95)
4042
vec96 = ValueSelect(vec10, 1, 96)
@@ -43,18 +45,28 @@
4345
VarianceAnalysis(vec10, 1, 2, "N")
4446

4547

46-
print type(ExtractHistogram(vec95, 2))
48+
print(type(ExtractHistogram(vec95, 2)))
4749

48-
Compare(ExtractHistogram(vec95, 2), ExtractHistogram(vec96, 2), ExtractHistogram(vec97, 2), "N")
49-
#Plot(ExtractHistogram(vec95, 2), ExtractHistogram(vec96, 2), ExtractHistogram(vec97, 2))
50+
Compare(
51+
ExtractHistogram(vec95, 2),
52+
ExtractHistogram(vec96, 2),
53+
ExtractHistogram(vec97, 2),
54+
"N",
55+
)
56+
# Plot(ExtractHistogram(vec95, 2), ExtractHistogram(vec96, 2), ExtractHistogram(vec97, 2))
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5158
ContingencyTable(vec10, 1, 4)
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# one-way variance analysis based on ranks
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5562
VarianceAnalysis(vec10, 1, 4, "O")
56-
Compare(ExtractHistogram(vec95, 4), ExtractHistogram(vec96, 4), ExtractHistogram(vec97, 4), "O")
63+
Compare(
64+
ExtractHistogram(vec95, 4),
65+
ExtractHistogram(vec96, 4),
66+
ExtractHistogram(vec97, 4),
67+
"O",
68+
)
5769
Plot(ExtractHistogram(vec95, 4), ExtractHistogram(vec96, 4), ExtractHistogram(vec97, 4))
5870

59-
#Plot(ExtractHistogram(vec95, 5), ExtractHistogram(vec96, 5), ExtractHistogram(vec97, 5))
60-
#Plot(ExtractHistogram(vec95, 6), ExtractHistogram(vec96, 6), ExtractHistogram(vec97, 6))
71+
# Plot(ExtractHistogram(vec95, 5), ExtractHistogram(vec96, 5), ExtractHistogram(vec97, 5))
72+
# Plot(ExtractHistogram(vec95, 6), ExtractHistogram(vec96, 6), ExtractHistogram(vec97, 6))

‎doc/pyplots/example_oak_6.py‎

Lines changed: 50 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -14,29 +14,32 @@
1414
#
1515
#########################################################################
1616
"""
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1718
__revision__ = "$Id: test_exploratory.py 8676 2010-04-20 15:28:46Z cokelaer $"
1819

20+
from os.path import join as pj
21+
1922
from openalea.sequence_analysis import *
20-
from openalea.sequence_analysis.estimate import Estimate
21-
from openalea.sequence_analysis.data import path
2223
from openalea.sequence_analysis import get_shared_data as path
23-
from os.path import join as pj
24-
seq0 = Sequences(pj(path ,"chene_sessile_15pa.seq"))
24+
from openalea.sequence_analysis.data import path
25+
from openalea.sequence_analysis.estimate import Estimate
2526

26-
#Plot(seq0, ViewPoint="Data")
27+
seq0 = Sequences(pj(path("chene_sessile_15pa.seq")))
28+
29+
# Plot(seq0, ViewPoint="Data")
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2831

2932
# change of unit for the variable diameter of the annual shoot
3033

3134
marginal3 = ExtractHistogram(seq0, "Value", 3)
32-
#Plot(Cluster(marginal3, "Information", 0.75))
33-
#Plot(Cluster(marginal3, "Information", 0.61))
34-
#Plot(Cluster(marginal3, "Step", 10))
35+
# Plot(Cluster(marginal3, "Information", 0.75))
36+
# Plot(Cluster(marginal3, "Information", 0.61))
37+
# Plot(Cluster(marginal3, "Step", 10))
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3639
vec10 = Vectors(seq0)
3740

3841
# plot of the average sequence
39-
#Plot(Regression(vec10, "MovingAverage", 1, 2, [1]))
42+
# Plot(Regression(vec10, "MovingAverage", 1, 2, [1]))
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4144
vec95 = ValueSelect(vec10, 1, 95)
4245
vec96 = ValueSelect(vec10, 1, 96)
@@ -45,36 +48,58 @@
4548
VarianceAnalysis(vec10, 1, 2, "N")
4649

4750

48-
print type(ExtractHistogram(vec95, 2))
51+
print(type(ExtractHistogram(vec95, 2)))
4952

50-
Compare(ExtractHistogram(vec95, 2), ExtractHistogram(vec96, 2), ExtractHistogram(vec97, 2), "N")
51-
#Plot(ExtractHistogram(vec95, 2), ExtractHistogram(vec96, 2), ExtractHistogram(vec97, 2))
53+
Compare(
54+
ExtractHistogram(vec95, 2),
55+
ExtractHistogram(vec96, 2),
56+
ExtractHistogram(vec97, 2),
57+
"N",
58+
)
59+
# Plot(ExtractHistogram(vec95, 2), ExtractHistogram(vec96, 2), ExtractHistogram(vec97, 2))
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5361
ContingencyTable(vec10, 1, 4)
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5563
# one-way variance analysis based on ranks
5664

5765
VarianceAnalysis(vec10, 1, 4, "O")
58-
Compare(ExtractHistogram(vec95, 4), ExtractHistogram(vec96, 4), ExtractHistogram(vec97, 4), "O")
59-
#Plot(ExtractHistogram(vec95, 4), ExtractHistogram(vec96, 4), ExtractHistogram(vec97, 4))
66+
Compare(
67+
ExtractHistogram(vec95, 4),
68+
ExtractHistogram(vec96, 4),
69+
ExtractHistogram(vec97, 4),
70+
"O",
71+
)
72+
# Plot(ExtractHistogram(vec95, 4), ExtractHistogram(vec96, 4), ExtractHistogram(vec97, 4))
6073

61-
#Plot(ExtractHistogram(vec95, 5), ExtractHistogram(vec96, 5), ExtractHistogram(vec97, 5))
62-
#Plot(ExtractHistogram(vec95, 6), ExtractHistogram(vec96, 6), ExtractHistogram(vec97, 6))
74+
# Plot(ExtractHistogram(vec95, 5), ExtractHistogram(vec96, 5), ExtractHistogram(vec97, 5))
75+
# Plot(ExtractHistogram(vec95, 6), ExtractHistogram(vec96, 6), ExtractHistogram(vec97, 6))
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6477
vec11 = ValueSelect(vec10, 4, 1)
6578
vec12 = ValueSelect(vec10, 4, 2)
6679
vec13 = ValueSelect(vec10, 4, 3, 4)
6780

68-
#Plot(ExtractHistogram(vec11, 2), ExtractHistogram(vec12, 2), ExtractHistogram(vec13, 2))
69-
#Plot(ExtractHistogram(vec11, 5), ExtractHistogram(vec12, 5), ExtractHistogram(vec13, 5))
70-
71-
mixt20 = Estimate(ExtractHistogram(vec10, 2), "MIXTURE", "NB", "NB", "NB", "NB", NbComponent="Estimated")
81+
# Plot(ExtractHistogram(vec11, 2), ExtractHistogram(vec12, 2), ExtractHistogram(vec13, 2))
82+
# Plot(ExtractHistogram(vec11, 5), ExtractHistogram(vec12, 5), ExtractHistogram(vec13, 5))
83+
84+
mixt20 = Estimate(
85+
ExtractHistogram(vec10, 2),
86+
"MIXTURE",
87+
"NB",
88+
"NB",
89+
"NB",
90+
"NB",
91+
NbComponent="Estimated",
92+
)
7293
Display(mixt20)
7394
Plot(mixt20)
7495
Plot(ExtractDistribution(mixt20, "Mixture"))
7596

76-
mixt21 = Estimate(ExtractHistogram(vec10, 5), "MIXTURE", "NB", "NB", "NB", "NB", NbComponent="Estimated")
77-
78-
79-
80-
97+
mixt21 = Estimate(
98+
ExtractHistogram(vec10, 5),
99+
"MIXTURE",
100+
"NB",
101+
"NB",
102+
"NB",
103+
"NB",
104+
NbComponent="Estimated",
105+
)

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