diff --git a/README b/README
index 71f6bfd589c92b6f17da40d045abd67a6aacb175..1d8ea5d83e3b1aee6266a9fc1342880878e610bf 100644
--- a/README
+++ b/README
@@ -1,87 +1,132 @@
+|build status| |coverage report|
-[](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
-[](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
+Introduction
+============
-# Introduction
+The Wind Energy Toolbox (or ``wetb``, pronounce as wee-tee-bee) is a
+collection of Python scripts that facilitate working with (potentially a
+lot) of HAWC2, HAWCStab2, FAST or other text input based simulation
+tools.
-The Wind Energy Toolbox (or ```wetb```, pronounce as wee-tee-bee) is a collection
-of Python scripts that facilitate working with (potentially a lot) of HAWC2,
-HAWCStab2, FAST or other text input based simulation tools.
-
-Note that this toolbox is very much a WIP (work in progress). For example,
-some of the functions in the [prepost](#prepost) module have a similar functions
-in [Hawc2io](wetb/hawc2/Hawc2io.py). These different implementations will be
-merged in due time.
+Note that this toolbox is very much a WIP (work in progress). For
+example, some of the functions in the `prepost <#prepost>`__ module have
+a similar functions in `Hawc2io <wetb/hawc2/Hawc2io.py>`__. These
+different implementations will be merged in due time.
Both Python2 and Python3 are supported.
-# Installation
-
-For a more detailed overview, see: [docs/install](docs/install.md)
-
-
-# Contents of WindEnergyToolbox, [wetb](wetb)
-
-### Overview
-
-- [hawc2](#hawc2)
-- [gtsdf](#gtsdf)
-- [fatigue_tools](#fatigue_tools)
-- [wind](#wind)
-- [dlc](#dlc)
-- [prepost](#prepost)
-- [fast](#fast)
-- [utils](#utils)
-
-### [hawc2](wetb/hawc2)
-- [Hawc2io](wetb/hawc2/Hawc2io.py): Read binary, ascii and flex result files
-- [sel_file](wetb/hawc2/sel_file.py): Read/write *.sel (sensor list) files
-- [htc_file](wetb/hawc2/htc_file.py): Read/write/manipulate htc files
-- [ae_file](wetb/hawc2/ae_file.py): Read AE (aerodynamic blade layout) files
-- [pc_file](wetb/hawc2/pc_file.py): Read PC (profile coefficient) files
-- [shear_file](wetb/hawc2/shear_file.py): Create user defined shear file
-- [at_time_file](wetb/hawc2/at_time_file.py): Read at output_at_time files
-- [log_file](wetb/hawc2/log_file.py): Read and interpret log files
-- [ascii2bin](wetb/hawc2/ascii2bin): Compress HAWC2 ascii result files to binary
-
-### [gtsdf](wetb/gtsdf)
-General Time Series Data Format, a binary hdf5 data format for storing time series data.
-- [gtsdf](wetb/gtsdf/gtsdf.py): read/write/append gtsdf files
-- [unix_time](wetb/gtsdf/unix_time.py): convert between datetime and unix time (seconds since 1/1/1970)
-
-### [fatigue_tools](wetb/fatigue_tools)
-- [fatigue](wetb/fatigue_tools/fatigue.py): Rainflow counting, cycle matrix and equivalent loads
-- [bearing_damage](wetb/fatigue_tools/bearing_damage.py): Calculate a comparable measure of bearing damage
-
-### [wind](wetb/wind)
-- [shear](wetb/wind/shear.py): Calculate and fit wind shear
-
-### [dlc](wetb/dlc)
-Module for working with "Design load cases" (Code independent)
-- [high_level](wetb/dlc/high_level.py) Class for working with the highlevel dlc excell sheet
-
-### [prepost](wetb/prepost)
-Module for creating an arbitrary number of HAWC2 simulations, and optionally
-corresponding execution scripts for a PBS Torque cluster (Linux), simple bash
-(Linux), or Windows batch scripts. A post-processing module is also included
-that calculates statistical parameters, performs rainflow counting for fatigue
-load calculations, and create load envelopes.
+Installation
+============
+
+- `Simple user <docs/install.md>`__
+- `Developer/contributor <docs/developer-guide.md>`__
+
+Contents of WindEnergyToolbox, `wetb <wetb>`__
+==============================================
+
+Overview
+~~~~~~~~
+
+- `hawc2 <#hawc2>`__
+- `gtsdf <#gtsdf>`__
+- `fatigue\_tools <#fatigue_tools>`__
+- `wind <#wind>`__
+- `dlc <#dlc>`__
+- `prepost <#prepost>`__
+- `fast <#fast>`__
+- `utils <#utils>`__
+
+`hawc2 <wetb/hawc2>`__
+~~~~~~~~~~~~~~~~~~~~~~
+
+- `Hawc2io <wetb/hawc2/Hawc2io.py>`__: Read binary, ascii and flex
+ result files
+- `sel\_file <wetb/hawc2/sel_file.py>`__: Read/write \*.sel (sensor
+ list) files
+- `htc\_file <wetb/hawc2/htc_file.py>`__: Read/write/manipulate htc
+ files
+- `ae\_file <wetb/hawc2/ae_file.py>`__: Read AE (aerodynamic blade
+ layout) files
+- `pc\_file <wetb/hawc2/pc_file.py>`__: Read PC (profile coefficient)
+ files
+- `st\_file <wetb/hawc2/st_file.py>`__: Read ST (structural properties)
+ files
+- `shear\_file <wetb/hawc2/shear_file.py>`__: Create user defined shear
+ file
+- `at\_time\_file <wetb/hawc2/at_time_file.py>`__: Read at
+ output\_at\_time files
+- `log\_file <wetb/hawc2/log_file.py>`__: Read and interpret log files
+- `ascii2bin <wetb/hawc2/ascii2bin>`__: Compress HAWC2 ascii result
+ files to binary
+
+`gtsdf <wetb/gtsdf>`__
+~~~~~~~~~~~~~~~~~~~~~~
+
+General Time Series Data Format, a binary hdf5 data format for storing
+time series data. - `gtsdf <wetb/gtsdf/gtsdf.py>`__: read/write/append
+gtsdf files - `unix\_time <wetb/gtsdf/unix_time.py>`__: convert between
+datetime and unix time (seconds since 1/1/1970)
+
+`fatigue\_tools <wetb/fatigue_tools>`__
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- `fatigue <wetb/fatigue_tools/fatigue.py>`__: Rainflow counting, cycle
+ matrix and equivalent loads
+- `bearing\_damage <wetb/fatigue_tools/bearing_damage.py>`__: Calculate
+ a comparable measure of bearing damage
+
+`wind <wetb/wind>`__
+~~~~~~~~~~~~~~~~~~~~
+
+- `shear <wetb/wind/shear.py>`__: Calculate and fit wind shear
+
+`dlc <wetb/dlc>`__
+~~~~~~~~~~~~~~~~~~
+
+Module for working with "Design load cases" (Code independent) -
+`high\_level <wetb/dlc/high_level.py>`__ Class for working with the
+highlevel dlc excell sheet
+
+`prepost <wetb/prepost>`__
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Module for creating an arbitrary number of HAWC2 simulations, and
+optionally corresponding execution scripts for a PBS Torque cluster
+(Linux), simple bash (Linux), or Windows batch scripts. A
+post-processing module is also included that calculates statistical
+parameters, performs rainflow counting for fatigue load calculations,
+and create load envelopes.
Additional documentation can be found here:
-- [Auto-generation of Design Load Cases](docs/howto-make-dlcs.md)
-- [How to use the Statistics DataFrame](docs/using-statistics-df.md)
-- [Generate DLB spreadsheets](docs/generate-spreadsheet.md)
-
-
-### [fast](wetb/fast)
-Tools for working with NREL's FAST code (An aeroelastic computer-aided engineering (CAE) tool for horizontal axis wind turbines)
-- [fast_io](wetb/fast/fast_io.py): Read binary and ascii result files
-
-### [utils](wetb/utils)
-Other functions
-- [geometry](wetb/utils/geometry.py): Different kind of geometry conversion functions
-- [process_exec](wetb/utils/process_exec.py): Run system command in subprocess
-- [timing](wetb/utils/timing.py): Decorators for evaluating execution time of functions
-- [caching](wetb/utils/caching.py): Decorators to create cached (calculate once) functions and properties
-
+- `Getting started with DLBs <docs/getting-started-with-dlbs.md>`__
+
+ - `Generate DLB spreadsheets <docs/generate-spreadsheet.md>`__
+ - `Auto-generation of Design Load Cases <docs/howto-make-dlcs.md>`__
+ - `House rules for storing results on
+ ``mimer/hawc2sim`` <docs/houserules-mimerhawc2sim.md>`__
+ - `How to use the Statistics
+ DataFrame <docs/using-statistics-df.md>`__
+
+`fast <wetb/fast>`__
+~~~~~~~~~~~~~~~~~~~~
+
+Tools for working with NREL's FAST code (An aeroelastic computer-aided
+engineering (CAE) tool for horizontal axis wind turbines) -
+`fast\_io <wetb/fast/fast_io.py>`__: Read binary and ascii result files
+
+`utils <wetb/utils>`__
+~~~~~~~~~~~~~~~~~~~~~~
+
+Other functions - `geometry <wetb/utils/geometry.py>`__: Different kind
+of geometry conversion functions -
+`process\_exec <wetb/utils/process_exec.py>`__: Run system command in
+subprocess - `timing <wetb/utils/timing.py>`__: Decorators for
+evaluating execution time of functions -
+`caching <wetb/utils/caching.py>`__: Decorators to create cached
+(calculate once) functions and properties
+
+.. |build status| image:: https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/badges/master/build.svg
+ :target: https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master
+.. |coverage report| image:: https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/badges/master/coverage.svg
+ :target: https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master
diff --git a/README.md b/README.md
index 99450330f46c42d32e59182d82259a3487b0ac44..715fc334c9b296316c7eccc7c94d71d0d376672b 100644
--- a/README.md
+++ b/README.md
@@ -71,10 +71,11 @@ load calculations, and create load envelopes.
Additional documentation can be found here:
-- [Auto-generation of Design Load Cases](docs/howto-make-dlcs.md)
-- [How to use the Statistics DataFrame](docs/using-statistics-df.md)
-- [Generate DLB spreadsheets](docs/generate-spreadsheet.md)
-
+- [Getting started with DLBs](docs/getting-started-with-dlbs.md)
+ - [Generate DLB spreadsheets](docs/generate-spreadsheet.md)
+ - [Auto-generation of Design Load Cases](docs/howto-make-dlcs.md)
+ - [House rules for storing results on ```mimer/hawc2sim```](docs/houserules-mimerhawc2sim.md)
+ - [How to use the Statistics DataFrame](docs/using-statistics-df.md)
### [fast](wetb/fast)
Tools for working with NREL's FAST code (An aeroelastic computer-aided engineering (CAE) tool for horizontal axis wind turbines)
diff --git a/docs/developer-guide.md b/docs/developer-guide.md
index 8156fe0e38f85985661f008f89a1aa5720004a06..708d90652080cf7007325e5f0064c72a734628f0 100644
--- a/docs/developer-guide.md
+++ b/docs/developer-guide.md
@@ -58,6 +58,7 @@ is a gui integrated into the windows explorer.
## Install Python
+
For all platforms we recommend that you download and install the Anaconda -
a professional grade, full blown scientific Python distribution.
@@ -157,8 +158,7 @@ Install the necessary Python dependencies using the conda package manager:
```
>> conda install setuptools_scm future h5py pytables pytest pytest-cov nose sphinx blosc pbr paramiko
>> conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl psutil pandoc
->> conda install -c conda-forge pyscaffold pypandoc sshtunnel --no-deps
->> conda install --channel https://conda.anaconda.org/pbrod twine --no-deps
+>> conda install -c conda-forge pyscaffold sshtunnel twine pypandoc --no-deps
```
Note that ```--no-deps``` avoids that newer packages from the channel
@@ -167,6 +167,11 @@ channel. Depending on which packages get overwritten, this might brake your
Anaconda root environment. As such, using ```--no-deps``` should be
used for safety (especially when operating from the root environment).
+Note that:
+
+- With Python 2.7, blosc fails to install.
+- With Python 3.6, twine, pypandoc fails to install.
+
## Get wetb
@@ -195,6 +200,34 @@ above for the ```conda-forge``` channel: it is to avoid that pip will replace
newer packages compared to the ones as available in the ```Anaconda``` channel.
+## Run tests
+
+Note that the test should be executed from a clean repository and which is not
+used as a development installation with ```pip install -e .```. For example,
+create a clone of your local git repository in which your development takes
+place, but name the top level folder to something else:
+
+```
+>> git clone WindEnergyToolbox/ wetb_tests
+>> cd wetb_tests
+```
+
+In order to make sure your git repository is clean, this will remove all
+untracked files, and undo all untracked changes. WARNING: you will loose all
+untracked files and changes!!
+```
+>> git clean -df & git checkout .
+```
+
+Now we have clean repository that is not used as a development installation
+directory, and we simply track our own local development git repository.
+Use ```git pull``` to get the latest local commits.
+
+```
+>> python -m pytest --cov=wetb
+```
+
+
## Contributions
If you make a change in the toolbox, that others can benefit from please make a merge request.
diff --git a/docs/howto-make-dlcs.md b/docs/howto-make-dlcs.md
index e9623a4b733a88ae2c49704d3fad418cb257f069..9e2db0e02878b38789312f8327470d4f0b32a90f 100644
--- a/docs/howto-make-dlcs.md
+++ b/docs/howto-make-dlcs.md
@@ -454,7 +454,7 @@ tags:
* ```[MannAlfaEpsilon]```
* ```[MannL]```
* ```[MannGamma]```
-* ```[tu_seed]```
+* ```[seed]```
* ```[turb_nr_u]``` : number of grid points in the u direction
* ```[turb_nr_v]``` : number of grid points in the v direction
* ```[turb_nr_w]``` : number of grid points in the w direction
diff --git a/setup.cfg b/setup.cfg
index 067c278a30fecfa5f91d5d995563b045048335d3..e287a0de26861609e3a471d3983825bffa2209e3 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -15,6 +15,7 @@ classifiers = Development Status :: 4 - Beta,
Programming Language :: Python :: 3.3,
Programming Language :: Python :: 3.4,
Programming Language :: Python :: 3.5,
+ Programming Language :: Python :: 3.6,
Environment :: Console,
Intended Audience :: Education,
Intended Audience :: Science/Research,
diff --git a/setup.py b/setup.py
index 368d369cda4e8a41f9348e793f5c8f2fdc436fbc..21fe89c4fe556521732d566f8d8f3d033161db7a 100644
--- a/setup.py
+++ b/setup.py
@@ -14,7 +14,7 @@ from setuptools import setup
try:
from pypandoc import convert_file
- read_md = lambda f: convert_file(f, 'rst')
+ read_md = lambda f: convert_file(f, 'rst', format='md')
except ImportError:
print("warning: pypandoc module not found, could not convert Markdown to RST")
read_md = lambda f: open(f, 'r').read()
diff --git a/wetb/prepost/Simulations.py b/wetb/prepost/Simulations.py
index 5a24ef095c5a2fb8047e43bdcee8ea6c79273d13..ad22964dcbb270fde671d6143b54772c75741d5e 100755
--- a/wetb/prepost/Simulations.py
+++ b/wetb/prepost/Simulations.py
@@ -553,7 +553,7 @@ def run_local(cases, silent=False, check_log=True):
def prepare_launch(iter_dict, opt_tags, master, variable_tag_func,
- write_htc=True, runmethod='local', verbose=False,
+ write_htc=True, runmethod='none', verbose=False,
copyback_turb=True, msg='', silent=False, check_log=True,
update_cases=False, ignore_non_unique=False, wine_appendix='',
run_only_new=False, windows_nr_cpus=2, qsub='',
@@ -603,11 +603,14 @@ def prepare_launch(iter_dict, opt_tags, master, variable_tag_func,
verbose : boolean, default=False
- runmethod : {'local' (default),'thyra','gorm','local-script','none'}
+ runmethod : {'none' (default),'pbs','linux-script','local',
+ 'local-ram', 'windows-script'}
Specify how/what to run where. For local, each case in cases is
- run locally via python directly. If set to 'local-script' a shell
+ run locally via python directly. If set to 'linux-script' a shell
script is written to run all cases locally sequential. If set to
- 'thyra' or 'gorm', PBS scripts are written to the respective server.
+ 'pbs', PBS scripts are written for a cluster (e.g. Gorm/jess).
+ A Windows batch script is written in case of windows-script, and is
+ used in combination with windows_nr_cpus.
msg : str, default=''
A descriptive message of the simulation series is saved at
@@ -1010,12 +1013,12 @@ def launch(cases, runmethod='none', verbose=False, copyback_turb=True,
verbose : boolean, default=False
- runmethod : {'none' (default),'jess','gorm','linux-script','local',
+ runmethod : {'none' (default),'pbs','linux-script','local',
'local-ram', 'windows-script'}
Specify how/what to run where. For local, each case in cases is
run locally via python directly. If set to 'linux-script' a shell
script is written to run all cases locally sequential. If set to
- 'jess' or 'gorm', PBS scripts are written to the respective server.
+ 'pbs', PBS scripts are written for a cluster (e.g. Gorm/jess).
A Windows batch script is written in case of windows-script, and is
used in combination with windows_nr_cpus.
@@ -1032,11 +1035,11 @@ def launch(cases, runmethod='none', verbose=False, copyback_turb=True,
local_shell_script(cases, sim_id)
elif runmethod == 'windows-script':
local_windows_script(cases, sim_id, nr_cpus=windows_nr_cpus)
- elif runmethod in ['jess','gorm']:
+ elif runmethod in ['pbs','jess','gorm']:
# create the pbs object
- pbs = PBS(cases, server=runmethod, short_job_names=short_job_names,
+ pbs = PBS(cases, short_job_names=short_job_names, pyenv=pyenv,
pbs_fname_appendix=pbs_fname_appendix, qsub=qsub,
- verbose=verbose, silent=silent, pyenv=pyenv)
+ verbose=verbose, silent=silent)
pbs.wine_appendix = wine_appendix
pbs.copyback_turb = copyback_turb
pbs.pbs_out_dir = pbs_out_dir
@@ -1049,8 +1052,8 @@ def launch(cases, runmethod='none', verbose=False, copyback_turb=True,
elif runmethod == 'none':
pass
else:
- msg = 'unsupported runmethod, valid options: local, local-script, ' \
- 'linux-script, windows-script, local-ram, none'
+ msg = 'unsupported runmethod, valid options: local, linux-script, ' \
+ 'windows-script, local-ram, none, pbs'
raise ValueError(msg)
@@ -1402,7 +1405,7 @@ class HtcMaster(object):
# create all the necessary directories
for dirkey in dirkeys:
- if self.tags[dirkey]:
+ if isinstance(self.tags[dirkey], str):
path = os.path.join(self.tags['[run_dir]'], self.tags[dirkey])
if not os.path.exists(path):
os.makedirs(path)
@@ -1430,7 +1433,7 @@ class HtcMaster(object):
# copy special files with changing file names
if '[ESYSMooring_init_fname]' in self.tags:
- if self.tags['[ESYSMooring_init_fname]'] is not None:
+ if isinstance(self.tags['[ESYSMooring_init_fname]'], str):
fname_source = self.tags['[ESYSMooring_init_fname]']
fname_target = 'ESYSMooring_init.dat'
shutil.copy2(model_root + fname_source,
@@ -1922,9 +1925,8 @@ class PBS(object):
such as the turbulence file and folder, htc folder and others
"""
- def __init__(self, cases, server='gorm', qsub='time', silent=False,
- pbs_fname_appendix=True, short_job_names=True, verbose=False,
- pyenv='wetb_py3'):
+ def __init__(self, cases, qsub='time', silent=False, pyenv='wetb_py3',
+ pbs_fname_appendix=True, short_job_names=True, verbose=False):
"""
Define the settings here. This should be done outside, but how?
In a text file, paramters list or first create the object and than set
@@ -1953,7 +1955,6 @@ class PBS(object):
case_id will be used as job name.
"""
- self.server = server
self.verbose = verbose
self.silent = silent
self.pyenv = pyenv
@@ -1962,14 +1963,9 @@ class PBS(object):
self.wine = self.winebase + 'wine'
self.winenumactl = self.winebase + 'numactl --physcpubind=$CPU_NR wine'
- if server == 'gorm':
- self.maxcpu = 1
- self.secperiter = 0.012
- elif server == 'jess':
- self.maxcpu = 1
- self.secperiter = 0.012
- else:
- raise UserWarning('server support only for jess or gorm')
+ # TODO: based on a certain host/architecture you can change these
+ self.maxcpu = 1
+ self.secperiter = 0.012
# determine at runtime if winefix has to be ran
self.winefix = ' _HOSTNAME_=`hostname`\n'
@@ -4007,11 +4003,11 @@ class Cases(object):
return stats_df, Leq_df, AEP_df
def statistics(self, new_sim_id=False, silent=False, ch_sel=None,
- tags=['[turb_seed]','[windspeed]'], calc_mech_power=False,
+ tags=['[seed]','[windspeed]'], calc_mech_power=False,
save=True, m=[3, 4, 6, 8, 10, 12], neq=None, no_bins=46,
ch_fatigue={}, update=False, add_sensor=None,
chs_resultant=[], i0=0, i1=None, saveinterval=1000,
- csv=True, suffix=None, A=None,
+ csv=True, suffix=None, A=None, add_sigs={},
ch_wind=None, save_new_sigs=False, xlsx=False):
"""
Calculate statistics and save them in a pandas dataframe. Save also
@@ -4024,7 +4020,7 @@ class Cases(object):
If defined, only add defined channels to the output data frame.
The list should contain valid channel names as defined in ch_dict.
- tags : list, default=['[turb_seed]','[windspeed]']
+ tags : list, default=['[seed]','[windspeed]']
Select which tag values from cases should be included in the
dataframes. This will help in selecting and identifying the
different cases.
@@ -4034,6 +4030,10 @@ class Cases(object):
needs to be calculated. When set to None, ch_fatigue = ch_sel,
and hence all channels will have a fatigue analysis.
+ add_sigs : dict, default={}
+ channel name, expression key/value paires. For example,
+ '[p1-p1-node-002-forcevec-z]*3 + [p1-p1-node-002-forcevec-y]'
+
chs_resultant
add_sensor
@@ -4129,6 +4129,8 @@ class Cases(object):
df_dict = None
add_stats = True
+ # for finding [] tags
+ regex = re.compile('(\\[.*?\\])')
for ii, (cname, case) in enumerate(self.cases.items()):
@@ -4165,6 +4167,26 @@ class Cases(object):
sig_size = self.res.N # len(self.sig[i0:i1,0])
new_sigs = np.ndarray((sig_size, 0))
+ for name, expr in add_sigs.items():
+ channel_tags = regex.findall(expr)
+ # replace all sensor names with expressions
+ template = "self.sig[:,self.res.ch_dict['{}']['chi']]"
+ for chan in channel_tags:
+ # first remove the [] from the tag
+ # FIXME: fails when the same channel occurs more than once
+ expr = expr.replace(chan, chan[1:-1])
+ expr = expr.replace(chan[1:-1], template.format(chan[1:-1]))
+
+ sig_add = np.ndarray((len(self.sig[:,0]), 1))
+ sig_add[:,0] = eval(expr)
+
+ ch_dict_new[name] = {}
+ ch_dict_new[name]['chi'] = i_new_chans
+ ch_df_new = add_df_row(ch_df_new, **{'chi':i_new_chans,
+ 'ch_name':name})
+ i_new_chans += 1
+ new_sigs = np.append(new_sigs, sig_add, axis=1)
+
if add_sensor is not None:
chi1 = self.res.ch_dict[add_sensor['ch1_name']]['chi']
chi2 = self.res.ch_dict[add_sensor['ch2_name']]['chi']
@@ -4305,10 +4327,9 @@ class Cases(object):
df_new_sigs = pd.DataFrame(new_sigs, columns=keys)
respath = os.path.join(case['[run_dir]'], case['[res_dir]'])
resfile = case['[case_id]']
- fname = os.path.join(respath, resfile + '_postres.h5')
+ fname = os.path.join(respath, resfile + '_postres.csv')
print(' saving post-processed res: %s...' % fname, end='')
- df_new_sigs.to_hdf(fname, 'table', mode='w', format='table',
- complevel=9, complib=self.complib)
+ df_new_sigs.to_csv(fname, sep='\t')
print('done!')
del df_new_sigs
@@ -4892,7 +4913,7 @@ class Cases(object):
return df_AEP
- def stats2dataframe(self, ch_sel=None, tags=['[turb_seed]','[windspeed]']):
+ def stats2dataframe(self, ch_sel=None, tags=['[seed]','[windspeed]']):
"""
Convert the archaic statistics dictionary of a group of cases to
a more convienent pandas dataframe format.
@@ -4910,7 +4931,7 @@ class Cases(object):
defined, only those channels are considered.
ch_sel[short name] = full ch_dict identifier
- tags : list, default=['[turb_seed]','[windspeed]']
+ tags : list, default=['[seed]','[windspeed]']
Select which tag values from cases should be included in the
dataframes. This will help in selecting and identifying the
different cases.
@@ -5357,7 +5378,7 @@ class MannTurb64(prepost.PBSScript):
* [MannAlfaEpsilon]
* [MannL]
* [MannGamma]
- * [tu_seed]
+ * [seed]
* [turb_nr_u]
* [turb_nr_v]
* [turb_nr_w]
@@ -5369,7 +5390,7 @@ class MannTurb64(prepost.PBSScript):
def __init__(self, silent=False):
super(MannTurb64, self).__init__()
- self.exe = 'time wine mann_turb_x64.exe'
+ self.exe = 'time WINEARCH=win64 WINEPREFIX=~/.wine wine mann_turb_x64.exe'
self.winefix = 'winefix\n'
# PBS configuration
self.umask = '0003'
@@ -5434,7 +5455,7 @@ class MannTurb64(prepost.PBSScript):
rpl = (float(case['[MannAlfaEpsilon]']),
float(case['[MannL]']),
float(case['[MannGamma]']),
- int(case['[tu_seed]']),
+ int(case['[seed]']),
int(case['[turb_nr_u]']),
int(case['[turb_nr_v]']),
int(case['[turb_nr_w]']),
diff --git a/wetb/prepost/dlcdefs.py b/wetb/prepost/dlcdefs.py
index 6443ab5d8a127e8ab4cc8fa451dfa018480e4487..e1a8b99b332ee0a419271d9ffa439f38fefff9f7 100644
--- a/wetb/prepost/dlcdefs.py
+++ b/wetb/prepost/dlcdefs.py
@@ -13,10 +13,9 @@ from future.utils import viewitems
from future import standard_library
standard_library.install_aliases()
-
-
import os
import unittest
+from glob import glob
import pandas as pd
@@ -28,7 +27,7 @@ def casedict2xlsx():
"""
-def configure_dirs(verbose=False):
+def configure_dirs(verbose=False, pattern_master='*_master_*'):
"""
Automatically configure required directories to launch simulations
"""
@@ -41,7 +40,7 @@ def configure_dirs(verbose=False):
PROJECT = P_RUN.split(os.sep)[-2]
sim_id = P_RUN.split(os.sep)[-1]
- master = find_master_file(P_SOURCE)
+ master = find_master_file(P_SOURCE, pattern=pattern_master)
if master is None:
raise ValueError('Could not find master file in htc/_master')
MASTERFILE = master
@@ -62,16 +61,30 @@ def configure_dirs(verbose=False):
def find_master_file(proot, htc_dir='htc', master_dir='_master',
- master_contains='_master_'):
+ pattern='*_master_*'):
"""
Find the master file name. It is assumed that the master file is in the
- folder _master, under htc, and contains _master_ in the file name.
+ folder _master, under htc, and contains _master_ in the file name. If
+ multiple files contain pattern, the last file of the sorted list is
+ returned.
+
+ Parameters
+ ----------
+
+ proot
+
+ htc_dir : str, default: htc
+
+ master_dir : str, default: _master
+
+ pattern : str, default: *_master_*
+
"""
- for root, dirs, files in os.walk(os.path.join(proot, htc_dir, master_dir)):
- for fname in files:
- if fname.find(master_contains) > -1:
- return fname
+ fpath_search = os.path.join(proot, htc_dir, master_dir, pattern)
+ files = glob(fpath_search)
+ if len(files) > 0:
+ return sorted(files)[-1]
return None
@@ -156,7 +169,7 @@ def tags_dlcs(master):
master.tags['[Windspeed]'] = 8
master.tags['[wdir]'] = 0 # used for the user defined wind
master.tags['[wdir_rot]'] = 0 # used for the windfield rotations
- master.tags['[tu_seed]'] = 0
+ master.tags['[seed]'] = None
master.tags['[tu_model]'] = 0
master.tags['[TI]'] = 0
master.tags['[Turb base name]'] = 'none'
@@ -350,8 +363,21 @@ def excel_stabcon(proot, fext='xlsx', pignore=None, pinclude=None, sheet=0,
elif tags_dict[str(key)].lower() == 'nan':
tags_dict[str(key)] = True
+ # FIXME: this horrible mess requires a nice and clearly defined
+ # tag spec/naming convention, and with special tag prefix
if '[Windspeed]' not in tags_dict and '[wsp]' in tags_dict:
tags_dict['[Windspeed]'] = tags_dict['[wsp]']
+ # avoid that any possible default tags from wetb will be used
+ # instead of the ones from the spreadsheet
+ if '[seed]' in tags_dict:
+ tags_dict['[tu_seed]'] = tags_dict['[seed]']
+ # in case people are using other turbulence tag names in the sheet
+ elif '[tu_seed]' in tags_dict:
+ tags_dict['[seed]'] = tags_dict['[tu_seed]']
+ elif '[turb_seed]' in tags_dict:
+ tags_dict['[seed]'] = tags_dict['[turb_seed]']
+ else:
+ raise KeyError('[seed] should be used as tag for turb. seed')
tags_dict['[Case folder]'] = tags_dict['[Case folder]'].lower()
tags_dict['[Case id.]'] = tags_dict['[Case id.]'].lower()
diff --git a/wetb/prepost/dlcplots.py b/wetb/prepost/dlcplots.py
index 7ba1f68fb7259396522171e239171eb9b13322ee..97cf0bf8ad8273192bcba61368fd1e8f4c138e2f 100644
--- a/wetb/prepost/dlcplots.py
+++ b/wetb/prepost/dlcplots.py
@@ -44,15 +44,15 @@ plt.rc('font', family='serif')
plt.rc('xtick', labelsize=10)
plt.rc('ytick', labelsize=10)
plt.rc('axes', labelsize=12)
-# do not use tex on Gorm
-if not socket.gethostname()[:2] in ['g-', 'je']:
+# do not use tex on Gorm and or Jess
+if not socket.gethostname()[:2] in ['g-', 'je', 'j-']:
plt.rc('text', usetex=True)
plt.rc('legend', fontsize=11)
plt.rc('legend', numpoints=1)
plt.rc('legend', borderaxespad=0)
-def merge_sim_ids(post_dirs, sim_ids, post_dir_save=False):
+def merge_sim_ids(sim_ids, post_dirs, post_dir_save=False):
"""
"""
# map the run_dir to the same order as the post_dirs, labels
@@ -502,7 +502,9 @@ def plot_dlc_stats(df_stats, plot_chans, fig_dir_base, labels=None,
# when only one of the channels was present, but the set is still
# complete.
# FIXME: what if both channels are present?
- if len(ch_names) > 1 and (lens[0] < 1) or (lens[1] < 1):
+ if len(ch_names) > 1 and (lens[0] < 1):
+ continue
+ elif len(ch_names) > 1 and len(lens)==2 and lens[1] < 1:
continue
print('start plotting: %s %s' % (str(dlc_name).ljust(7), ch_dscr))
diff --git a/wetb/prepost/dlctemplate.py b/wetb/prepost/dlctemplate.py
index dc5a6f430ba32580bff16c2c01c8e94b213e01f6..beb9d5424b28d5ff539b26b4d3ab1c6d202f0ef4 100644
--- a/wetb/prepost/dlctemplate.py
+++ b/wetb/prepost/dlctemplate.py
@@ -34,16 +34,12 @@ plt.rc('xtick', labelsize=10)
plt.rc('ytick', labelsize=10)
plt.rc('axes', labelsize=12)
# on Gorm tex printing doesn't work
-if socket.gethostname()[:2] == 'g-':
- RUNMETHOD = 'gorm'
-elif socket.gethostname()[:1] == 'j':
- RUNMETHOD = 'jess'
+if socket.gethostname()[:2] in ['g-', 'je', 'j-']:
+ RUNMETHOD = 'pbs'
else:
plt.rc('text', usetex=True)
# set runmethod based on the platform host
- if platform == "linux" or platform == "linux2":
- RUNMETHOD = 'local-script'
- elif platform == "darwin":
+ if platform in ["linux", "linux2", "darwin"]:
RUNMETHOD = 'linux-script'
elif platform == "win32":
RUNMETHOD = 'windows-script'
@@ -131,7 +127,7 @@ def master_tags(sim_id, runmethod='local', silent=False, verbose=False):
master.tags['[MannAlfaEpsilon]'] = 1.0
master.tags['[MannL]'] = 29.4
master.tags['[MannGamma]'] = 3.0
- master.tags['[tu_seed]'] = 0
+ master.tags['[seed]'] = None
master.tags['[turb_nr_u]'] = 8192
master.tags['[turb_nr_v]'] = 32
master.tags['[turb_nr_w]'] = 32
@@ -268,7 +264,8 @@ def variable_tag_func_mod1(master, case_id_short=False):
# =============================================================================
def launch_dlcs_excel(sim_id, silent=False, verbose=False, pbs_turb=False,
- runmethod=None, write_htc=True, zipchunks=False):
+ runmethod=None, write_htc=True, zipchunks=False,
+ walltime='04:00:00'):
"""
Launch load cases defined in Excel files
"""
@@ -307,6 +304,7 @@ def launch_dlcs_excel(sim_id, silent=False, verbose=False, pbs_turb=False,
master = master_tags(sim_id, runmethod=runmethod, silent=silent,
verbose=verbose)
master.tags['[sim_id]'] = sim_id
+ master.tags['[walltime]'] = walltime
master.output_dirs.append('[Case folder]')
master.output_dirs.append('[Case id.]')
@@ -336,13 +334,18 @@ def launch_dlcs_excel(sim_id, silent=False, verbose=False, pbs_turb=False,
if zipchunks:
# create chunks
# sort so we have minimal copying turb files from mimer to node/scratch
+ # note that walltime here is for running all cases assigned to the
+ # respective nodes. It is not walltime per case.
sorts_on = ['[DLC]', '[Windspeed]']
create_chunks_htc_pbs(cases, sort_by_values=sorts_on, ppn=20,
- nr_procs_series=9, processes=1,
- walltime='20:00:00', chunks_dir='zip-chunks-jess')
+ nr_procs_series=9, walltime='20:00:00',
+ chunks_dir='zip-chunks-jess')
create_chunks_htc_pbs(cases, sort_by_values=sorts_on, ppn=12,
- nr_procs_series=15, processes=1,
- walltime='20:00:00', chunks_dir='zip-chunks-gorm')
+ nr_procs_series=15, walltime='20:00:00',
+ chunks_dir='zip-chunks-gorm')
+
+ df = sim.Cases(cases).cases2df()
+ df.to_excel(os.path.join(POST_DIR, sim_id + '.xls'))
def post_launch(sim_id, statistics=True, rem_failed=True, check_logs=True,
@@ -385,6 +388,11 @@ def post_launch(sim_id, statistics=True, rem_failed=True, check_logs=True,
if statistics:
i0, i1 = 0, -1
+ # example for combination of signals
+# name = 'stress1'
+# expr = '[p1-p1-node-002-forcevec-z]*3 + [p1-p1-node-002-forcevec-y]'
+# add_sigs = {name:expr}
+
# in addition, sim_id and case_id are always added by default
tags = ['[Case folder]']
add = None
@@ -395,7 +403,7 @@ def post_launch(sim_id, statistics=True, rem_failed=True, check_logs=True,
update=update, saveinterval=saveinterval,
suffix=suffix, save_new_sigs=save_new_sigs,
csv=csv, m=m, neq=None, no_bins=no_bins,
- chs_resultant=[], A=A)
+ chs_resultant=[], A=A, add_sigs={})
# annual energy production
if AEP:
df_AEP = cc.AEP(df_stats, csv=csv, update=update, save=True)
@@ -486,7 +494,11 @@ if __name__ == '__main__':
'using the 64-bit Mann turbulence box generator. '
'This can be usefull if your turbulence boxes are too '
'big for running in HAWC2 32-bit mode. Only works on '
- 'Jess. ')
+ 'Jess.')
+ parser.add_argument('--walltime', default='04:00:00', type=str,
+ action='store', dest='walltime', help='Queue walltime '
+ 'for each case/pbs file, format: HH:MM:SS '
+ 'Default: 04:00:00')
opt = parser.parse_args()
# TODO: use arguments to determine the scenario:
@@ -526,7 +538,7 @@ if __name__ == '__main__':
if opt.prep:
print('Start creating all the htc files and pbs_in files...')
launch_dlcs_excel(sim_id, silent=False, zipchunks=opt.zipchunks,
- pbs_turb=opt.pbs_turb)
+ pbs_turb=opt.pbs_turb, walltime=opt.walltime)
# post processing: check log files, calculate statistics
if opt.check_logs or opt.stats or opt.fatigue or opt.envelopeblade or opt.envelopeturbine:
post_launch(sim_id, check_logs=opt.check_logs, update=False,
diff --git a/wetb/prepost/h2_vs_hs2.py b/wetb/prepost/h2_vs_hs2.py
index cd065486d076d1bd168c9183202cd2e47eaee165..8db023d5be593aef3564f3d3806206e23647d389 100644
--- a/wetb/prepost/h2_vs_hs2.py
+++ b/wetb/prepost/h2_vs_hs2.py
@@ -311,10 +311,10 @@ class Sims(object):
mt['[hawc2]'] = False
mt['[output]'] = False
mt['[copyback_files]'] = ['./*.ind', './*.pwr', './*.log',
- './*.cmb', './*.bea']
+ './*.cmb', './*.bea', './*.amp']
mt['[copyback_frename]'] = [mt['[res_dir]'], mt['[res_dir]'],
mt['[log_dir]'], mt['[res_dir]'],
- mt['[res_dir]']]
+ mt['[res_dir]'], mt['[res_dir]']]
if mt['[hs2_bladedeform_switch]']:
mt['[hs2_bladedeform]'] = 'bladedeform'
else:
@@ -347,32 +347,20 @@ class Sims(object):
relevant HAWC2 model
and assume we are in a simulation case of a certain turbine/project
"""
- (self.P_RUN, self.P_SOURCE, self.PROJECT,
- self.sim_id, self.P_MASTERFILE,
- self.MASTERFILE, self.POST_DIR) = dlcdefs.configure_dirs(verbose=verbose)
- def _set_path_config(self, runmethod='here'):
+ tmp = dlcdefs.configure_dirs(verbose=verbose)
+ (self.P_RUN, self.P_SOURCE, self.PROJECT, self.sim_id,
+ self.P_MASTERFILE, self.MASTERFILE, self.POST_DIR) = tmp
+
+ def _set_path_config(self, p_root_run='auto'):
"""
Set the path configuration into the tags
"""
- self.runmethod = runmethod
-
- if runmethod == 'here':
+ if p_root_run == 'auto':
self._set_path_auto_config()
- elif runmethod in ['local', 'local-script', 'none', 'local-ram']:
- self.p_root = '/home/dave/SimResults/h2_vs_hs2/'
- elif runmethod == 'windows-script':
- self.p_root = '/mnt/D16731/dave/Documents/_SimResults'
- elif runmethod == 'gorm':
- self.p_root = '/mnt/hawc2sim/h2_vs_hs2'
- elif runmethod == 'jess':
- self.p_root = '/mnt/hawc2sim/h2_vs_hs2'
else:
- msg='unsupported runmethod, options: none, local, gorm or opt'
- raise ValueError(msg)
-
- if not runmethod == 'here':
+ self.p_root = p_root_run
self.P_RUN = os.path.join(self.p_root, self.PROJECT, self.sim_id)
self.master.tags['[master_htc_file]'] = self.MASTERFILE
@@ -430,10 +418,11 @@ class Sims(object):
return iter_dict, opt_tags
- def create_inputs(self, iter_dict, opt_tags):
+ def create_inputs(self, iter_dict, opt_tags, runmethod='pbs'):
+ self.runmethod = runmethod
sim.prepare_launch(iter_dict, opt_tags, self.master, self._var_tag_func,
- write_htc=True, runmethod=self.runmethod, verbose=False,
+ write_htc=True, runmethod=runmethod, verbose=False,
copyback_turb=False, msg='', update_cases=False,
ignore_non_unique=False, run_only_new=False,
pbs_fname_appendix=False, short_job_names=False)
@@ -444,25 +433,7 @@ class Sims(object):
"""
tuning = hs2.ReadControlTuning()
tuning.read_parameters(fpath)
-
- tune_tags = {}
-
- tune_tags['[pi_gen_reg1.K]'] = tuning.pi_gen_reg1.K
-
- tune_tags['[pi_gen_reg2.I]'] = tuning.pi_gen_reg2.I
- tune_tags['[pi_gen_reg2.Kp]'] = tuning.pi_gen_reg2.Kp
- tune_tags['[pi_gen_reg2.Ki]'] = tuning.pi_gen_reg2.Ki
-
- tune_tags['[pi_pitch_reg3.Kp]'] = tuning.pi_pitch_reg3.Kp
- tune_tags['[pi_pitch_reg3.Ki]'] = tuning.pi_pitch_reg3.Ki
- tune_tags['[pi_pitch_reg3.K1]'] = tuning.pi_pitch_reg3.K1
- tune_tags['[pi_pitch_reg3.K2]'] = tuning.pi_pitch_reg3.K2
-
- tune_tags['[aero_damp.Kp2]'] = tuning.aero_damp.Kp2
- tune_tags['[aero_damp.Ko1]'] = tuning.aero_damp.Ko1
- tune_tags['[aero_damp.Ko2]'] = tuning.aero_damp.Ko2
-
- return tune_tags
+ return tuning.parameters2tags()
def post_processing(self, statistics=True, resdir=None, complib='blosc',
calc_mech_power=False):
@@ -485,23 +456,8 @@ class Sims(object):
# load the file saved in post_dir
cc = sim.Cases(post_dir, self.sim_id, rem_failed=False, complib=complib)
- if resdir is None:
- # we keep the run_dir as defined during launch
- run_root = None
- elif resdir in ['local', 'local-script', 'none', 'local-ram']:
- run_root = '/home/dave/SimResults'
- elif resdir == 'windows-script':
- run_root = '/mnt/D16731/dave/Documents/_SimResults'
- elif resdir == 'gorm':
- run_root = '/mnt/hawc2sim/h2_vs_hs2'
- elif resdir == 'jess':
- run_root = '/mnt/hawc2sim/h2_vs_hs2'
- else:
- run_root = None
- cc.change_results_dir(resdir)
-
- if isinstance(run_root, str):
- forcedir = os.path.join(run_root, self.PROJECT, self.sim_id)
+ if isinstance(resdir, str):
+ forcedir = os.path.join(resdir, self.PROJECT, self.sim_id)
cc.change_results_dir(forcedir)
cc.post_launch()
diff --git a/wetb/prepost/hawcstab2.py b/wetb/prepost/hawcstab2.py
index 1129dc7e0daf1299454975527580ef9ac5e0f3be..ec1c7020e1ec19c6284df9b0e192472b769e6df5 100644
--- a/wetb/prepost/hawcstab2.py
+++ b/wetb/prepost/hawcstab2.py
@@ -28,36 +28,40 @@ class dummy(object):
def __init__(self, name='dummy'):
self.__name__ = name
+regex_units = re.compile('(\\[.*?\\])')
-def ReadFileHAWCStab2Header(fname, widths):
+
+def ReadFileHAWCStab2Header(fname):
"""
Read a file with a weird HAWCStab2 header that starts with a #, and
includes the column number and units between square brackets.
"""
- regex = re.compile('(\\[.*?\\])')
-
- def _newformat(fname):
- df = pd.read_fwf(fname, header=0, widths=[20]*15)
- # find all units
- units = regex.findall(''.join(df.columns))
- df.columns = [k[:-2].replace('#', '').strip() for k in df.columns]
- return df, units
-
- def _oldformat(fname):
- df = pd.read_fwf(fname, header=0, widths=[14]*13)
- # find all units
- units = regex.findall(''.join(df.columns))
- df.columns = [k.replace('#', '').strip() for k in df.columns]
+ def _read(fname, header=0, widths=[20]*15, skipfooter=0):
+ df = pd.read_fwf(fname, header=header, widths=widths,
+ skipfooter=skipfooter)
+ units = regex_units.findall(''.join(df.columns))
return df, units
with open(fname) as f:
line = f.readline()
- if len(line) > 200:
- return _newformat(fname)
+ # when gradients are included in the output
+ if len(line) > 800:
+ df, units = _read(fname, header=1, widths=[30]*27)
+ # column name has the name, unit and column number in it...
+ df.columns = [k[:-2].replace('#', '').strip() for k in df.columns]
+ return df, units
+ elif len(line) > 200:
+ df, units = _read(fname, header=0, widths=[20]*15)
+ # column name has the name, unit and column number in it...
+ df.columns = [k[:-2].replace('#', '').strip() for k in df.columns]
+ return df, units
+ # older versions of HS2 seem to have two columns less
else:
- return _oldformat(fname)
+ df, units = _read(fname, header=0, widths=[14]*13)
+ df.columns = [k.replace('#', '').strip() for k in df.columns]
+ return df, units
class InductionResults(object):
@@ -99,7 +103,7 @@ class results(object):
return res
def load_pwr_df(self, fname):
- return ReadFileHAWCStab2Header(fname, [20]*15)
+ return ReadFileHAWCStab2Header(fname)
def load_cmb(self, fname):
cmb = np.loadtxt(fname)
@@ -149,6 +153,32 @@ class results(object):
self.ind = InductionResults()
self.ind.read(fname)
+ def load_amp(self, fname):
+
+ with open(fname) as f:
+ line = f.readline()
+
+ width = 14
+ nrcols = int((len(line)-1)/width)
+ # first columns has one extra character
+ # col nr1: rotor speed, col nr2: radius
+ widths = [width+1] + [width]*(nrcols-1)
+ # last line is empty
+ df = pd.read_fwf(fname, header=2, widths=widths, skipfooter=1)
+ units = regex_units.findall(''.join(df.columns))
+ # no column number in the column name
+ # since U_x, u_y, phase and theta will be repeated as many times as
+ # there are modes, add the mode number in the column name
+ columns = [k.replace('#', '').strip() for k in df.columns]
+ nrmodes = int((len(columns) - 2 )/6)
+ for k in range(nrmodes):
+ for i in range(6):
+ j = 2+k*6+i
+ columns[j] = columns[j].split('.')[0] + ' nr%i' % (k+1)
+ df.columns = columns
+
+ return df, units
+
def load_operation(self, fname):
operation = np.loadtxt(fname, skiprows=1)
@@ -341,12 +371,42 @@ class ReadControlTuning(object):
else:
self.parse_line(line, controller)
- # set some parameters to zero for the linear case
+ # set some parameters to zero for the linear case, or when aerodynamic
+ # gain scheduling is not used
if not hasattr(self.pi_pitch_reg3, 'K2'):
setattr(self.pi_pitch_reg3, 'K2', 0.0)
+ if not hasattr(self.aero_damp, 'Kp2'):
+ setattr(self.aero_damp, 'Kp2', 0.0)
+ if not hasattr(self.aero_damp, 'Ko1'):
+ setattr(self.aero_damp, 'Ko1', 0.0)
if not hasattr(self.aero_damp, 'Ko2'):
setattr(self.aero_damp, 'Ko2', 0.0)
+ def parameters2tags(self):
+ """Convert the tuning parameters into a dictionary whos keys are
+ compatible with tag names in a HAWC2 master file.
+ """
+
+ tune_tags = {}
+
+ tune_tags['[pi_gen_reg1.K]'] = self.pi_gen_reg1.K
+
+ tune_tags['[pi_gen_reg2.I]'] = self.pi_gen_reg2.I
+ tune_tags['[pi_gen_reg2.Kp]'] = self.pi_gen_reg2.Kp
+ tune_tags['[pi_gen_reg2.Ki]'] = self.pi_gen_reg2.Ki
+ tune_tags['[pi_gen_reg2.Kd]'] = 0.0
+
+ tune_tags['[pi_pitch_reg3.Kp]'] = self.pi_pitch_reg3.Kp
+ tune_tags['[pi_pitch_reg3.Ki]'] = self.pi_pitch_reg3.Ki
+ tune_tags['[pi_pitch_reg3.K1]'] = self.pi_pitch_reg3.K1
+ tune_tags['[pi_pitch_reg3.K2]'] = self.pi_pitch_reg3.K2
+
+ tune_tags['[aero_damp.Kp2]'] = self.aero_damp.Kp2
+ tune_tags['[aero_damp.Ko1]'] = self.aero_damp.Ko1
+ tune_tags['[aero_damp.Ko2]'] = self.aero_damp.Ko2
+
+ return tune_tags
+
if __name__ == '__main__':
diff --git a/wetb/prepost/misc.py b/wetb/prepost/misc.py
index d95b2b4fdc30686fada422ccf5930fa875e23b66..c6ce5759e02e3ad45abb38a248cc7d2443a2b3ea 100644
--- a/wetb/prepost/misc.py
+++ b/wetb/prepost/misc.py
@@ -24,6 +24,7 @@ import sys
import shutil
import unittest
import pickle
+import re
import numpy as np
import scipy as sp
@@ -786,7 +787,24 @@ def find_tags(fname):
"""
Find all unqiue tags in a text file.
"""
- pass
+
+ with open(fname, 'r') as f:
+ lines = f.readlines()
+
+ # regex for finding all tags in a line
+ regex = re.compile('(\\[.*?\\])')
+ tags_in_master = {}
+
+ for i, line in enumerate(lines):
+ # are there any tags on this line? Ignore comment AND label section
+ tags = regex.findall(line.split(';')[0].split('#')[0])
+ for tag in tags:
+ try:
+ tags_in_master[tag].append(i)
+ except KeyError:
+ tags_in_master[tag] = [i]
+
+ return tags_in_master
def read_mathematica_3darray(fname, shape=None, data=None, dtype=None):
diff --git a/wetb/prepost/mplutils.py b/wetb/prepost/mplutils.py
index 02e60e24a26c64b18b2f94ffeb9023f5e79a4ff3..08dcf1f990065ac67c932b4d1fc1de792c1ef374 100644
--- a/wetb/prepost/mplutils.py
+++ b/wetb/prepost/mplutils.py
@@ -24,7 +24,11 @@ import numpy as np
import matplotlib as mpl
# use a headless backend
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigCanvas
-#import wafo
+# wafo is an optional dependency only required for non default PSD peak marking
+try:
+ import wafo
+except ImportError:
+ pass
def make_fig(nrows=1, ncols=1, figsize=(12,8), dpi=120):
@@ -117,6 +121,15 @@ def one_legend(*args, **kwargs):
"""First list all the axes as arguments. Any keyword arguments will be
passed on to ax.legend(). Legend will be placed on the last axes that was
passed as an argument.
+
+ Parameters
+ ----------
+
+ Returns
+ -------
+
+ legend
+
"""
# or more general: not only simple line plots (bars, hist, ...)
objs = []
@@ -267,7 +280,8 @@ def match_yticks(ax1, ax2, nr_ticks_forced=None, extend=False):
def time_psd(results, labels, axes, alphas=[1.0, 0.7], colors=['k-', 'r-'],
NFFT=None, res_param=250, f0=0, f1=None, nr_peaks=10, min_h=15,
- mark_peaks=True):
+ mark_peaks=False, xlabels=['frequency [Hz]', 'time [s]'],
+ ypos_peaks=[0.04, 0.9], ypos_peaks_delta=0.12):
"""
Plot time series and the corresponding PSD of the channel.
@@ -297,7 +311,6 @@ def time_psd(results, labels, axes, alphas=[1.0, 0.7], colors=['k-', 'r-'],
"""
axes = axes.ravel()
- ypos = [0.04, 0.90]
for i, res in enumerate(results):
time, data = res
@@ -328,14 +341,15 @@ def time_psd(results, labels, axes, alphas=[1.0, 0.7], colors=['k-', 'r-'],
if mark_peaks:
axes[0] = peaks(axes[0], freqs[i0:i1], Pxx[i0:i1], fn_max=f1,
nr_peaks=nr_peaks, col_line=col[:1],
- ypos_delta=0.04, bbox_alpha=0.5, col_text='w',
- ypos_mean=ypos[i], min_h=min_h)
+ ypos_delta=ypos_peaks_delta, bbox_alpha=0.5,
+ ypos_mean=ypos_peaks[i], min_h=min_h, col_text='w')
# plotting time series
axes[1].plot(time, data, col, label=label, alpha=alpha)
axes[0].set_yscale('log')
- axes[0].set_xlabel('frequency [Hz]')
- axes[1].set_xlabel('time [s]')
+ if isinstance(xlabels, list):
+ axes[0].set_xlabel(xlabels[0])
+ axes[1].set_xlabel(xlabels[1])
for ax in axes:
leg = ax.legend(loc='best', borderaxespad=0)
# leg is None when no labels have been defined
diff --git a/wetb/prepost/simchunks.py b/wetb/prepost/simchunks.py
index 4e4d560313bf88756054d24e0dd5981a4bca617b..0fc2f8eff7501e3ccc26cb14de71518a6c2df8f1 100644
--- a/wetb/prepost/simchunks.py
+++ b/wetb/prepost/simchunks.py
@@ -32,10 +32,9 @@ import pandas as pd
from wetb.prepost.Simulations import Cases
-def create_chunks_htc_pbs(cases, sort_by_values=['[Windspeed]'], ppn=20,
- nr_procs_series=9, processes=1, queue='workq',
- walltime='24:00:00', chunks_dir='zip-chunks-jess',
- pyenv='wetb_py3', i0=0):
+def create_chunks_htc_pbs(cases, sort_by_values=['[Windspeed]'], ppn=20, i0=0,
+ nr_procs_series=9, queue='workq', pyenv='wetb_py3',
+ walltime='24:00:00', chunks_dir='zip-chunks-jess'):
"""Group a large number of simulations htc and pbs launch scripts into
different zip files so we can run them with find+xargs on various nodes.
"""
@@ -187,7 +186,7 @@ def create_chunks_htc_pbs(cases, sort_by_values=['[Windspeed]'], ppn=20,
# =====================================================================
# activate the python environment
pbs += 'echo "activate python environment %s"\n' % pyenv
- pbs += 'source activate %s\n' % pyenv
+ pbs += 'source /home/python/miniconda3/bin/activate %s\n' % pyenv
# sometimes activating an environment fails due to a FileExistsError
# is this because it is activated at the same time on another node?
# check twice if the environment got activated for real
@@ -396,6 +395,10 @@ def create_chunks_htc_pbs(cases, sort_by_values=['[Windspeed]'], ppn=20,
except (FileExistsError, OSError):
pass
+ fpath = os.path.join(df['[run_dir]'].iloc[0], 'pbs_out_chunks')
+ if not os.path.exists(fpath):
+ os.makedirs(fpath)
+
df_iter = chunker(df, nr_procs_series*ppn)
sim_id = df['[sim_id]'].iloc[0]
run_dir = df['[run_dir]'].iloc[0]
diff --git a/wetb/prepost/tests/data/demo_dlc/ref/htc/DLCs/dlc01_demos.xlsx b/wetb/prepost/tests/data/demo_dlc/ref/htc/DLCs/dlc01_demos.xlsx
index 2725ebf94c486118c288c7b1bf73bfba9fb79afd..6b4bb2d9fe4f7b5b2e347ecb8da55e2cd3695669 100755
Binary files a/wetb/prepost/tests/data/demo_dlc/ref/htc/DLCs/dlc01_demos.xlsx and b/wetb/prepost/tests/data/demo_dlc/ref/htc/DLCs/dlc01_demos.xlsx differ
diff --git a/wetb/prepost/tests/data/demo_dlc/ref/pbs_in_turb/turb_s100_10ms.p b/wetb/prepost/tests/data/demo_dlc/ref/pbs_in_turb/turb_s100_10ms.p
index 79b15e566904b8e0b365b70c46c31bea42f99ea4..995b9af1d2669b3ed8d57c578ebb08c151d988c3 100644
--- a/wetb/prepost/tests/data/demo_dlc/ref/pbs_in_turb/turb_s100_10ms.p
+++ b/wetb/prepost/tests/data/demo_dlc/ref/pbs_in_turb/turb_s100_10ms.p
@@ -35,7 +35,7 @@ echo "------------------------------------------------------------------------"
echo "EXECUTION"
echo "------------------------------------------------------------------------"
-time wine mann_turb_x64.exe turb_s100_10ms 1.000000 29.400000 3.000000 100 8192 32 32 0.7812 6.5000 6.5000 1
+time WINEARCH=win64 WINEPREFIX=~/.wine wine mann_turb_x64.exe turb_s100_10ms 1.000000 29.400000 3.000000 100 8192 32 32 0.7812 6.5000 6.5000 1
### wait for jobs to finish
wait
diff --git a/wetb/prepost/tests/data/demo_dlc/ref/pbs_in_turb/turb_s101_11ms.p b/wetb/prepost/tests/data/demo_dlc/ref/pbs_in_turb/turb_s101_11ms.p
index 7997dc29dc535d9a5136282e8d8744b4d876a0d8..6372504ddce65b8599f6d4ee196d451f8411af30 100644
--- a/wetb/prepost/tests/data/demo_dlc/ref/pbs_in_turb/turb_s101_11ms.p
+++ b/wetb/prepost/tests/data/demo_dlc/ref/pbs_in_turb/turb_s101_11ms.p
@@ -35,7 +35,7 @@ echo "------------------------------------------------------------------------"
echo "EXECUTION"
echo "------------------------------------------------------------------------"
-time wine mann_turb_x64.exe turb_s101_11ms 1.000000 29.400000 3.000000 100 8192 32 32 0.8594 6.5000 6.5000 1
+time WINEARCH=win64 WINEPREFIX=~/.wine wine mann_turb_x64.exe turb_s101_11ms 1.000000 29.400000 3.000000 100 8192 32 32 0.8594 6.5000 6.5000 1
### wait for jobs to finish
wait
diff --git a/wetb/prepost/tests/data/demo_dlc/ref/prepost/remote.pkl b/wetb/prepost/tests/data/demo_dlc/ref/prepost/remote.pkl
index 424870abe4d235d40b0bc86884127247ace71cde..76f3458974d302669780c4e764e56dec5a7d545b 100644
Binary files a/wetb/prepost/tests/data/demo_dlc/ref/prepost/remote.pkl and b/wetb/prepost/tests/data/demo_dlc/ref/prepost/remote.pkl differ
diff --git a/wetb/prepost/tests/data/demo_dlc/ref/prepost/remote_tags.txt b/wetb/prepost/tests/data/demo_dlc/ref/prepost/remote_tags.txt
index eebe622e1cd2307810c65f8ed345bec9f81ebe5d..c9bef2a6ba10c1291db7d183aa091af4f542d6ec 100644
--- a/wetb/prepost/tests/data/demo_dlc/ref/prepost/remote_tags.txt
+++ b/wetb/prepost/tests/data/demo_dlc/ref/prepost/remote_tags.txt
@@ -50,6 +50,7 @@
[pbs_in_dir] : pbs_in/dlc01_demos/
[pbs_out_dir] : pbs_out/dlc01_demos/
[res_dir] : res/dlc01_demos/
+ [seed] : 0
[shear_exp] : 0
[staircase] : False
[t flap on] : -1
@@ -106,6 +107,7 @@
[pbs_in_dir] : pbs_in/dlc01_demos/
[pbs_out_dir] : pbs_out/dlc01_demos/
[res_dir] : res/dlc01_demos/
+ [seed] : 0
[shear_exp] : 0
[staircase] : False
[t flap on] : -1
@@ -162,6 +164,7 @@
[pbs_in_dir] : pbs_in/dlc01_demos/
[pbs_out_dir] : pbs_out/dlc01_demos/
[res_dir] : res/dlc01_demos/
+ [seed] : 100
[shear_exp] : 0
[staircase] : False
[t flap on] : -1
@@ -218,6 +221,7 @@
[pbs_in_dir] : pbs_in/dlc01_demos/
[pbs_out_dir] : pbs_out/dlc01_demos/
[res_dir] : res/dlc01_demos/
+ [seed] : 100
[shear_exp] : 0
[staircase] : False
[t flap on] : -1
diff --git a/wetb/prepost/tests/data/demo_dlc/source/demo_dlc_remote.zip b/wetb/prepost/tests/data/demo_dlc/source/demo_dlc_remote.zip
index 3c02a1d7a11acaeff10fdae72416c4856fcbc4bc..653dd7fa920d3d0154225072507087b8fbf3cfa0 100644
Binary files a/wetb/prepost/tests/data/demo_dlc/source/demo_dlc_remote.zip and b/wetb/prepost/tests/data/demo_dlc/source/demo_dlc_remote.zip differ
diff --git a/wetb/prepost/windIO.py b/wetb/prepost/windIO.py
index cb267752a3ea2974d0377ab80be53b81672d71f4..03b8e9a219236154d52ae98031749215b89f743d 100755
--- a/wetb/prepost/windIO.py
+++ b/wetb/prepost/windIO.py
@@ -98,8 +98,8 @@ class LogFile(object):
self.err_init[' Error opening PC data file'] = len(self.err_init)
# *** ERROR *** error reading mann turbulence
self.err_init[' *** ERROR *** error readin'] = len(self.err_init)
- # *** INFO *** The DLL subroutine
- self.err_init[' *** INFO *** The DLL subro'] = len(self.err_init)
+# # *** INFO *** The DLL subroutine
+# self.err_init[' *** INFO *** The DLL subro'] = len(self.err_init)
# ** WARNING: FROM ESYS ELASTICBAR: No keyword
self.err_init[' ** WARNING: FROM ESYS ELAS'] = len(self.err_init)
# *** ERROR *** DLL ./control/killtrans.dll could not be loaded - error!
@@ -643,6 +643,9 @@ class LoadResults(ReadHawc2):
of spaces, use colon (;) to seperate the different commands.
THIS IS STILL A WIP
+
+ see also issue #11:
+ https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues/11
"""
index = {}