From 13d6d2112360189204afd3ba8f84ecf85097047e Mon Sep 17 00:00:00 2001
From: Le Roux Erwan <erwan.le-roux@irstea.fr>
Date: Mon, 5 Nov 2018 16:50:19 +0100
Subject: [PATCH] [EXTREME FIT][GEV FIT] fix sourcing issue
---
extreme_estimator/R_fit/gev_fit/gev_marginal.py | 1 +
.../R_fit/gev_fit/{gev_fit.R => gev_mle_fit.R} | 0
extreme_estimator/R_fit/gev_fit/gev_mle_fit.py | 6 ++++--
extreme_estimator/R_fit/utils.py | 9 ++++++++-
4 files changed, 13 insertions(+), 3 deletions(-)
rename extreme_estimator/R_fit/gev_fit/{gev_fit.R => gev_mle_fit.R} (100%)
diff --git a/extreme_estimator/R_fit/gev_fit/gev_marginal.py b/extreme_estimator/R_fit/gev_fit/gev_marginal.py
index 424eecd0..8b15be58 100644
--- a/extreme_estimator/R_fit/gev_fit/gev_marginal.py
+++ b/extreme_estimator/R_fit/gev_fit/gev_marginal.py
@@ -6,6 +6,7 @@ def frechet_unitary_transformation(data, location, scale, shape):
Compute the unitary Frechet transformed data
(1 + \zeta \frac{z - \mu}{\sigma}) ^ {\frac{1}{\zeta}}
"""
+ # todo: there is already a function doing that in R
return (1 + shape * (data - location) / scale) ** (1 / shape)
diff --git a/extreme_estimator/R_fit/gev_fit/gev_fit.R b/extreme_estimator/R_fit/gev_fit/gev_mle_fit.R
similarity index 100%
rename from extreme_estimator/R_fit/gev_fit/gev_fit.R
rename to extreme_estimator/R_fit/gev_fit/gev_mle_fit.R
diff --git a/extreme_estimator/R_fit/gev_fit/gev_mle_fit.py b/extreme_estimator/R_fit/gev_fit/gev_mle_fit.py
index 5bfe53f3..e56280b3 100644
--- a/extreme_estimator/R_fit/gev_fit/gev_mle_fit.py
+++ b/extreme_estimator/R_fit/gev_fit/gev_mle_fit.py
@@ -1,9 +1,11 @@
import rpy2.robjects as ro
import numpy as np
import rpy2.robjects.numpy2ri as rpyn
-
+import os.path as op
# Defining some constants
+from extreme_estimator.R_fit.utils import get_associated_r_file
+
GEV_SCALE = 'scale'
GEV_LOCATION = 'loc'
GEV_SHAPE = 'shape'
@@ -16,7 +18,7 @@ def mle_gev(x_gev: np.ndarray, start_loc=0, start_scale=1, start_shape=0):
x_gev = rpyn.numpy2ri(x_gev)
r.assign('x_gev', x_gev)
r.assign('python_wrapping', True)
- r.source(file="/home/erwan/Documents/projects/spatiotemporalextremes/extreme_estimator/gev_fit/gev_fit.extreme_estimator")
+ r.source(file=get_associated_r_file(python_filepath=op.abspath(__file__)))
res = r.mle_gev(loc=start_loc, scale=start_scale, shape=start_shape)
mle_params = dict(r.attr(res, 'coef').items())
return mle_params
diff --git a/extreme_estimator/R_fit/utils.py b/extreme_estimator/R_fit/utils.py
index 8e308400..87a89fb9 100644
--- a/extreme_estimator/R_fit/utils.py
+++ b/extreme_estimator/R_fit/utils.py
@@ -1,16 +1,23 @@
+import os.path as op
import rpy2.robjects as ro
import pandas as pd
import numpy as np
import rpy2.robjects.numpy2ri as npr
-def get_loaded_r():
+def get_loaded_r() -> ro.R:
r = ro.r
ro.numpy2ri.activate()
r.library('SpatialExtremes')
return r
+def get_associated_r_file(python_filepath: str) -> str:
+ assert op.exists(python_filepath)
+ r_filepath = python_filepath.replace('.py', '.R')
+ assert op.exists(r_filepath), r_filepath
+ return r_filepath
+
# def conversion_to_FloatVector(data):
# """Convert DataFrame or numpy array into FloatVector for r"""
# if isinstance(data, pd.DataFrame):
--
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