diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 307784f8f8a750aabb68dd96c0239d5553084404..03a585734c5ee4377274a68ab3756ecda0efd92e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,4 +4,6 @@ before_script:
test-3.4:
image: mmpe/wetb
script:
- - python3 setup.py test
\ No newline at end of file
+ #- python3 setup.py test
+ - python3 -m coverage run ./tests/run_pytest.py
+ - python3 -m coverage report -m
\ No newline at end of file
diff --git a/README.md b/README.md
index b8f2fbbb678a74baacf870f4f16355e27f5c5cc1..f019bc546495292a060e55d267991173a96ff24f 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,6 @@
+[](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
+[](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
# Introduction
The Wind Energy Toolbox (or ```wetb```, pronounce as wee-tee-bee) is a collection
diff --git a/wetb/prepost/Simulations.py b/wetb/prepost/Simulations.py
index a60e9b286b71e729a4e24443853342d5834034f9..b2ccffdf089f4f1d5b38d1a53c5dd08c33129159 100755
--- a/wetb/prepost/Simulations.py
+++ b/wetb/prepost/Simulations.py
@@ -1058,6 +1058,19 @@ def post_launch(cases, save_iter=False, silent=False, suffix=None,
----------
cases : either a string (path to file) or the cases itself
+
+ save_iter : boolean, default=False
+ Set to True to save the number of iterations per time step in
+ *.iter file (in the same folder as the logfile)
+
+ path_errorlog : str, default=None
+ Root path of the error logfiles. If set to None (default), the
+ value set in the [run_dir] tag is used as the root folder of the
+ logfiles.
+
+ suffix : str, default=None
+ If not None, the suffix will be appended to file name of the error
+ log analysis file as follows: "ErrorLog_suffix.csv".
"""
# TODO: finish support for default location of the cases and file name
@@ -3563,20 +3576,41 @@ class Cases(object):
launch(self.cases, runmethod=runmethod, verbose=verbose, silent=silent,
check_log=check_log, copyback_turb=copyback_turb)
- def post_launch(self, save_iter=False, copy_pbs_failed=True, suffix=None,
+ def post_launch(self, save_iter=False, pbs_failed_path=False, suffix=None,
path_errorlog=None, silent=False):
"""
Post Launching Maintenance
check the logs files and make sure result files are present and
accounted for.
+
+ Parameters
+ ----------
+
+ save_iter : boolean, default=False
+ Set to True to save the number of iterations per time step in
+ *.iter file (in the same folder as the logfile)
+
+ pbs_failed_path : str, default=False
+ If not False, specify the path to which the *.p files of the
+ failed cases should be copied to. For example, the dlctemplate
+ will set this value to "pbs_in_fail".
+
+ path_errorlog : str, default=None
+ Root path of the error logfiles. If set to None (default), the
+ value set in the [run_dir] tag is used as the root folder of the
+ logfiles.
+
+ suffix : str, default=None
+ If not None, the suffix will be appended to file name of the error
+ log analysis file as follows: "ErrorLog_suffix.csv".
"""
# TODO: integrate global post_launch in here
self.cases_fail = post_launch(self.cases, save_iter=save_iter,
suffix=suffix, path_errorlog=path_errorlog)
- if copy_pbs_failed:
- copy_pbs_in_failedcases(self.cases_fail, path='pbs_in_fail',
+ if pbs_failed_path is not False:
+ copy_pbs_in_failedcases(self.cases_fail, path=pbs_failed_path,
silent=silent)
if self.rem_failed:
@@ -4609,6 +4643,12 @@ class Cases(object):
# ---------------------------------------------------------------------
# column definitions
# ---------------------------------------------------------------------
+ # FIXME: for backward compatibility, the column name of the unique
+ # channel name has been changed in the past....
+ if 'unique_ch_name' in dfs.columns:
+ chan_col_name = 'unique_ch_name'
+ else:
+ chan_col_name = 'channel'
# available material constants
ms, cols = [], []
for key in dfs:
@@ -4617,7 +4657,7 @@ class Cases(object):
# when multiple DLC cases are included, add extra cols to identify each
# DLC group. Make a copy, because extra_cols does not get re-initiated
# when defined as an optional keyword argument
- extra_cols_ = copy.copy(extra_cols + ['channel'])
+ extra_cols_ = copy.copy(extra_cols + [chan_col_name])
cols = copy.copy(ms)
cols.extend(extra_cols_)
# ---------------------------------------------------------------------
@@ -4628,7 +4668,7 @@ class Cases(object):
dfs = dfs.set_index('[case_id]')
# which rows to keep: a
# select for each channel all the cases
- for grname, gr in dfs.groupby(dfs.channel):
+ for grname, gr in dfs.groupby(dfs[chan_col_name]):
# if one m has any nan's, assume none of them are good and throw
# away
# if np.isnan(gr[ms[0]].values).any():
diff --git a/wetb/prepost/dlctemplate.py b/wetb/prepost/dlctemplate.py
index 22a1899a14fc17d8c0be6debd2e77c702b787b2e..07213815eefd7877dac5d103a8ec99fcf3ad66b2 100644
--- a/wetb/prepost/dlctemplate.py
+++ b/wetb/prepost/dlctemplate.py
@@ -266,7 +266,7 @@ def post_launch(sim_id, statistics=True, rem_failed=True, check_logs=True,
m=[1, 3, 4, 5, 6, 8, 10, 12, 14], neq=None, no_bins=46,
years=20.0, fatigue=True, A=None, AEP=False,
save_new_sigs=False, envelopeturbine=False, envelopeblade=False,
- save_iter=False):
+ save_iter=False, pbs_failed_path=False):
# =========================================================================
# check logfiles, results files, pbs output files
@@ -286,7 +286,7 @@ def post_launch(sim_id, statistics=True, rem_failed=True, check_logs=True,
cc.cases[case]['[run_dir]'] = force_dir
if check_logs:
- cc.post_launch(save_iter=save_iter)
+ cc.post_launch(save_iter=save_iter, pbs_failed_path=pbs_failed_path)
elif rem_failed:
cc.remove_failed()
@@ -360,6 +360,11 @@ if __name__ == '__main__':
dest='prep', help='create htc, pbs, files')
parser.add_argument('--check_logs', action='store_true', default=False,
dest='check_logs', help='check the log files')
+ parser.add_argument('--pbs_failed_path', default='pbs_in_fail', type=str,
+ action='store', dest='pbs_failed_path',
+ help='Copy pbs launch files of the failed cases to a '
+ 'new directory in order to prepare a re-run. Default '
+ 'value: pbs_in_failed.')
parser.add_argument('--stats', action='store_true', default=False,
dest='stats', help='calculate statistics and 1Hz '
'equivalent loads')
@@ -443,7 +448,7 @@ if __name__ == '__main__':
force_dir=P_RUN, saveinterval=2000, csv=opt.csv,
statistics=opt.stats, years=opt.years, neq=opt.neq,
fatigue=opt.fatigue, A=opt.rotarea, AEP=opt.AEP,
- no_bins=opt.no_bins,
+ no_bins=opt.no_bins, pbs_failed_path=opt.pbs_failed_path,
save_new_sigs=opt.save_new_sigs, save_iter=False,
envelopeturbine=opt.envelopeturbine,
envelopeblade=opt.envelopeblade)
diff --git a/wetb/prepost/misc.py b/wetb/prepost/misc.py
index f25b97897d3060b4591d7160c9c4590cc6aba107..d95b2b4fdc30686fada422ccf5930fa875e23b66 100644
--- a/wetb/prepost/misc.py
+++ b/wetb/prepost/misc.py
@@ -19,22 +19,17 @@ from future import standard_library
standard_library.install_aliases()
from builtins import object
-
-
-#print(*objects, sep=' ', end='\n', file=sys.stdout)
import os
import sys
import shutil
import unittest
import pickle
-#from xlrd import open_workbook
import numpy as np
import scipy as sp
from scipy import optimize as opt
from scipy import stats
-#import scipy.interpolate
-#import scipy.ndimage
+from scipy.interpolate import griddata as interp
from matplotlib import pyplot as plt
import pandas as pd
@@ -950,6 +945,9 @@ def histfit(hist, bin_edges, xnew):
http://nbviewer.ipython.org/url/xweb.geos.ed.ac.uk/~jsteven5/blog/
fitting_distributions_from_percentiles.ipynb
+ Calculate the CDF of given PDF, and fit a lognorm distribution onto the
+ CDF. This obviously only works if your PDF is lognorm.
+
Parameters
----------
@@ -988,6 +986,87 @@ def histfit(hist, bin_edges, xnew):
return shape_out, scale_out, pdf_fit
+def histfit_arbritrary(edges, pdf, edges_new, resolution=100):
+ """Re-bin based on the CDF of a PDF. Assume normal distribution within
+ a bin to transform the CDF to higher resolution.
+
+ Parameters
+ ----------
+
+ edges : ndarray(n+1)
+ edges of the bins, inlcuding most left and right edges.
+
+ pdf : ndarray(n)
+ probability of the bins
+
+ edges_new : ndarray(m+1)
+ edges of the new bins
+
+ resolution : int
+ resolution of the intermediate CDF used for re-fitting.
+
+
+ Returns
+ -------
+
+ centers_new : ndarray(m)
+
+ widths_new : ndarray(m)
+
+ pdf_new : ndarray(m)
+
+ """
+
+ x_hd = np.ndarray((0,))
+ cdf_hd = np.ndarray((0,))
+ binw = np.ndarray((0,))
+
+ for i in range(len(pdf)):
+ # HD grid for x
+ x_inc = np.linspace(edges[i], edges[i+1], num=resolution)
+
+ # FIXME: let the distribution in a bin be a user configurable input
+ # define a distribution within the bin: norm
+ shape = 2.5
+ scale = shape*2/10
+ x_inc = np.linspace(0, scale*10, num=resolution)
+ cdf_inc = stats.norm.cdf(x_inc, shape, scale=scale)
+
+ # scale cdf_inc and x-coordinates
+ cdf_inc_scale = pdf[i] * cdf_inc / cdf_inc[-1]
+ binw = edges[i+1] - edges[i]
+ x_inc_scale = edges[i] + (binw * x_inc / x_inc[-1])
+
+ # add to the new hd corodinates and cdf
+ x_hd = np.append(x_hd, x_inc_scale)
+ if i == 0:
+ cdf_i = 0
+ else:
+ cdf_i = cdf_hd[-1]
+ cdf_hd = np.append(cdf_hd, cdf_inc_scale + cdf_i)
+
+# plt.plot(x_inc, cdf_inc)
+# plt.plot(x_inc_scale, cdf_inc_scale)
+
+ cdf_new = interp(x_hd, cdf_hd, edges_new)
+ # last point includes everything that comes after
+ cdf_new[-1] = 1
+ pdf_new = np.diff(cdf_new)
+ widths_new = np.diff(edges_new)
+ centers_new = widths_new + edges[0]
+ # the first bin also includes everything that came before
+ pdf_new[0] += cdf_new[0]
+ pdf_new /= pdf_new.sum()
+
+# plt.plot(x_hd, cdf_hd)
+# plt.plot(edges_new, cdf_new, 'rs')
+#
+# plt.bar(edges_new[:-1], pdf_new, width=widths_new, color='b')
+# plt.bar(edges[:-1], pdf, width=np.diff(edges), color='r', alpha=0.7)
+
+ return centers_new, widths_new, pdf_new
+
+
def hist_centers2edges(centers):
"""Given the centers of bins, return its edges and bin widths.
"""