.gitattributes

+*.bin filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -3,4 +3,30 @@ dist/*
 *.pyc
 *.pyd
 *egg-info*
+*.so
+.eggs
+doctrees
+docs/_build
+.project
+.pydevproject
+.settings/org.eclipse.core.resources.prefs
+wetb/gtsdf/tests/tmp
+wetb/dlc/tests/test_files/res_all
+wetb/dlc/tests/test_files/res2_all
+wetb/hawc2/ascii2bin/ascii2bin_dist
+wetb/hawc2/tests/test_files/htcfiles/tmp.htc
+wetb/hawc2/ascii2bin/tests/test_files/Hawc2ascii_bin.sel
+wetb/hawc2/ascii2bin/tests/test_files/Hawc2ascii_bin.dat
+wetb/prepost/tests/data/demo_dlc/remote*
+wetb/*/*/*.c
+.cache/
+tests/temp.htc
+**/tmp/*
 
+/wetb/fatigue_tools/rainflowcounting/compile.py
+/docs/api
+/htmlcov
+/docs/build
+/docs/source_old
+.ipynb_checkpoints
+/.pytest_cache/

.gitlab-ci.yml

+image: dtuwindenergy/wetb
+
+workflow:
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+      when: never
+    - when: always
+
+
+test:
+  image: continuumio/anaconda3:latest
+  stage:
+    test
+#  except:
+#    - test_pypi
+  variables:
+    GIT_SUBMODULE_STRATEGY: recursive
+  before_script:
+  #- git submodule sync --recursive
+  #- git submodule update --init --recursive
+  - python -m pip install .[all]
+  script:
+  - python3 -m pytest --cov-report term-missing:skip-covered --cov-report xml:coverage.xml --cov=wetb
+  tags:
+  - docker, linux, shared
+  coverage: /(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/
+  artifacts:
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+
+
+
+# ===== build documentation =====
+pages:  # "pages" is a job specifically for GitLab pages [1]
+  stage:  # build, test, deploy defined by default [2]
+    deploy
+  image: registry.windenergy.dtu.dk/hawc2/hawc2-binary/dockerimages/ubuntu_conda
+  script:  # use sphinx to build docs, move to public page
+  - pip install --upgrade pip
+  - pip install sphinx --upgrade
+  - pip install sphinx sphinx_rtd_theme
+  - pip install nbsphinx==0.3.5
+  - pip install git+https://github.com/vidartf/nbsphinx-link.git
+  - pip install -e .
+  - cd docs; make html
+  - cd ../; mv docs/build/html public/
+  artifacts:  # required for GitLab pages [1]
+    paths:
+    - public
+  only:  # only run for these branches
+  - master
+  - /^test_doc.*/
+  tags:  # only runners with this tag can do the job [3]
+  - python
+  allow_failure: true
+
+# Deploy package to local repository
+
+upload_package_local:
+  image: continuumio/anaconda3:latest
+  tags:
+    - docker, linux, shared
+  stage: deploy
+  needs:
+  - job: build_wheel
+    artifacts: true
+  - job: test
+    artifacts: false
+
+  script:
+    - pip install --upgrade twine packaging
+    - TWINE_PASSWORD=${CI_JOB_TOKEN} TWINE_USERNAME=gitlab-ci-token python -m twine upload --verbose --repository-url ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi dist/*
+  
+  rules:
+    - if: $CI_COMMIT_TAG != null
+      when: always
+    - if: $CI_COMMIT_BRANCH == "master"
+      when: always
+    - if: $CI_COMMIT_BRANCH != "master"
+      when: manual
+      allow_failure: true
+
+
+
+  # ===== BUILD WHEELS AND UPLOAD TO PYPI =====
+upload_package_pypi:
+  image: continuumio/anaconda3:latest
+  tags:
+    - docker, linux, shared
+  stage: deploy
+  needs:
+  - job: build_wheel
+    artifacts: true
+  - job: test
+    artifacts: false
+
+  script:
+    - pip install --upgrade twine packaging
+    - twine upload dist/* -u $TWINE_USERNAME -p $TWINE_PASSWORD
+  only:
+    - tags
+    - test_pypi
+
+
+build_wheel:
+  stage: build
+  tags:
+    - linux, docker, shared
+  image: registry.windenergy.dtu.dk/hawc2/hawc2-binary/dockerimages/ubuntu_conda
+  before_script:
+    - git config --global --add safe.directory ${CI_PROJECT_DIR}
+  script:
+    - pip wheel . --wheel-dir=dist
+  artifacts:
+    paths:
+      - dist/wetb*.whl
+    expire_in: "1d"

.gitmodules

+[submodule "TestFiles"]
+	path = TestFiles
+	url = https://gitlab.windenergy.dtu.dk/toolbox/TestFiles.git

.pypirc

+[distutils]
+index-servers=
+    pypi
+    #testpypi # include this line for testing
+
+[testpypi]
+#repository: https://test.pypi.org/legacy/ # use this line when testing
+repository: https://upload.pypi.org/legacy/
+username: DTUWindEnergy

AUTHORS.rst

@@ -3,4 +3,5 @@ Developers
 ==========
 
 * Mads Mølgaard Pedersen
-* David Verelst
+* David R.S. Verelst
+* Carlo Tibaldi

CONTRIBUTING.md

+Contributions
+-------------
+
+If you make a change in the toolbox, that others can benefit from please make a merge request.
+
+If you can, please submit a merge request with the fix or improvements including tests.
+
+The workflow to make a merge request is as follows:
+
+
+-Create a feature branch, branch away from master
+-Write tests and code
+-Push the commit(s) to your fork
+-Submit a merge request (MR) to the master branch of
+-Link any relevant issues in the merge request description and leave a comment on them with a link back to the MR
+-Your tests should run as fast as possible, and if it uses test files, these files should be as small as possible.
+-Please keep the change in a single MR as small as possible. Split the functionality if you can
\ No newline at end of file

README

+|build status| |coverage report|
+
+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.
+
+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
+============
+
+-  `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:
+
+-  `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

README.md

+
+[![build status](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/badges/master/build.svg)](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
+[![coverage report](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/badges/master/coverage.svg)](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
+[![pypi status](https://img.shields.io/pypi/v/wetb.png)](https://pypi.python.org/pypi/wetb)
+
+# 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.
+
+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
+
+See documentation.
+
+# Documentation
+
+[https://toolbox.pages.windenergy.dtu.dk/WindEnergyToolbox/](https://toolbox.pages.windenergy.dtu.dk/WindEnergyToolbox/)
+
+
 # Contents of WindEnergyToolbox, [wetb](wetb)
 
+### Overview
+
 - [hawc2](#hawc2)
 - [gtsdf](#gtsdf)
 - [fatigue_tools](#fatigue_tools)
 - [wind](#wind)
 - [dlc](#dlc)
+- [prepost](#prepost)
 - [fast](#fast)
-- [functions](#functions)
+- [utils](#utils)
 
-------------------------------------------------------------------------------------
-### [hawc2](wetb/hawc2) 
+### [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
+- [ae_file](wetb/hawc2/ae_file.py): Read/write/manipulate AE (aerodynamic blade layout) files
+- [pc_file](wetb/hawc2/pc_file.py): Read/write/manipulate PC (profile coefficient) files
+- [st_file](wetb/hawc2/st_file.py): Read/write/manipulate 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
@@ -26,24 +56,39 @@ General Time Series Data Format, a binary hdf5 data format for storing time seri
 - [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 equvivalent loads
+- [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 
+- [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:
+
+- [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
 
-### [functions](wetb/functions)
+### [utils](wetb/utils)
 Other functions
-- [geometry](wetb/functions/geometry.py): Different kind of geometry conversion functions
-- [process_exec](wetb/functions/process_exec.py): Run system command in subprocess
-- [timing](wetb/functions/timing.py): Decorators for evaluating execution time of functions
-- [caching](wetb/functions/caching.py): Decorators to create cached (calculate once) functions and properties
\ No newline at end of file
+- [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
+

TestFiles @ 167b16d8

+Subproject commit 167b16d8f1a26161ebc5a258c62389777d133489

docker/Dockerfile

+FROM continuumio/anaconda3:latest
+MAINTAINER Mikkel Friis-Møller <mikf@dtu.dk>
+
+RUN apt-get update && \
+    apt-get install make && \
+    apt-get install libgl1-mesa-glx -y && \
+    apt-get install gcc gfortran -y
+
+RUN conda update -y conda && \
+    conda install -y sphinx_rtd_theme && \
+	conda install setuptools_scm mock h5py pytables pytest pytest-cov nose sphinx blosc pbr paramiko && \
+	conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl psutil pandoc twine pypandoc && \
+	conda install -c conda-forge pyscaffold sshtunnel --no-deps && \
+    conda clean -y --all
+
+RUN pip install --upgrade pip && \
+	pip install --no-cache-dir git+https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox.git

docker/Makefile

+# build image
+docker build -t dtuwindenergy/wetb ./
+# or pull from docker hub
+  
+# create container
+docker create -it --name wetb dtuwindenergy/wetb
+
+# start container
+docker start wetb
+
+# enter container with bash prompt
+docker exec -it wetb bash
+
+# push
+docker push dtuwindenergy/wetb
+
+#checkout single branch for testing:
+git clone --single-branch --branch test_pypi https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox.git
+
+#Copy local folder into docker container:
+docker cp "C:\Sandbox\Git\WindEnergyToolbox\." wetb:/WETB/

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = TOPFARM
+SOURCEDIR     = .
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

docs/bladed/bladed2hawc.ipynb

+%% Cell type:markdown id: tags:
+
+# Bladed to HAWC2 model conversion formulation
+
+%% Cell type:markdown id: tags:
+
+# Coordinate transformation: <br>
+
+The parameters belonging to HAWC2 are showed by $*^H$ and the parameters belonging to Bladed are showed by $*^B$.
+
+$ ----------------------------------$<br>
+The blade root coordinate systems of the codes can be transfromed as:
+
+\begin{equation}
+\begin{bmatrix} x^H \\ y^H \\ z^H \end{bmatrix} = \begin{bmatrix} 0 & -1 & 0 \\ 1 & 0 & 0 \\ 0 & 0 & 1 \end{bmatrix} \begin{bmatrix} x^B \\ y^B \\ z^B \end{bmatrix}
+\end{equation}
+
+The transformation matrix is called $R^{H2B}$.
+
+$ ----------------------------------$<br>
+
+The total rotation angle is expressed by $\theta_{CS}^{B}$ which is comupted as:<br>
+
+$\theta_{CS}^{B}$ = -$\theta_p^B$ - $\beta_{\alpha}^B$ <br>
+
+**BE CAREFUL !!!** -> Bladed positive pitch/twist definition are in negative z direction. <br>
+
+Transformation matrix $R^{B2CS}$ from Bladed local cross-section coordinates to the rotor coordinate system. <br>
+
+\begin{equation}
+\begin{bmatrix} x^B \\ y^B \\ z^B \end{bmatrix}  = \begin{bmatrix} cos(\theta_{CS}^{B}) & sin(\theta_{CS}^{B}) & 0 \\ -sin(\theta_{CS}^{B}) & cos(\theta_{CS}^{B}) & 0 \\ 0 & 0 & 1 \end{bmatrix} \begin{bmatrix} x^B_{CS} \\ y^B_{CS} \\ z^B_{CS} \end{bmatrix}
+\end{equation}
+
+$ ----------------------------------$<br>
+
+Total transformation from Bladed local coordinates to HAWC2 can be written as: <br>
+
+\begin{equation}
+\begin{bmatrix} x^H \\ y^H \\ z^H \end{bmatrix} = R^{H2B} R^{B2CS} \begin{bmatrix} x^B_{CS} \\ y^B_{CS} \\ z^B_{CS} \end{bmatrix}
+\end{equation}
+
+$ ----------------------------------$
+
+%% Cell type:markdown id: tags:
+
+## Center positions <br>
+
+HAWC2 defines elastic, shear and mass center according to the half chord (*c2_def*) location in its st files
+whereas Bladed measures center positions from leading edge position. The center positions ($x_{LE}^B$ and $y_{LE}^B$) can be defined with respect to the half chord ($x_{c2}^B$ and $y_{c2}^B$) in Bladed coordinate system as: <br>
+
+$x_{c2}^B$ = $x_{LE}^B$ <br>
+$y_{c2}^B$ = $y_{LE}^B$ - c/2 <br>
+
+where *c* is the chord length. <br>
+
+These coordinates can be transformed to HAWC2 coordinate system by multiplying them with $R^{H2B}$.
+
+
+%% Cell type:markdown id: tags:
+
+## Inertia conversion <br>
+
+Bladed has total inertia value *Ip* and radius of gyration ratio *RGRATIO* in its input file. <br>
+
+\begin{equation}
+RGRATIO = \dfrac{RG_y}{RG_x}
+\end{equation}
+
+\begin{equation}
+RG_x^2 = \dfrac{I_x}{m} \; , \; RG_y^2 = \dfrac{I_y}{m}
+\end{equation}
+
+where m is mass and $I_x$ is the mass moment of inertia with respect to x axis.
+
+\begin{equation}
+Ip = I_x + RGRATIO^2 \times I_x
+\end{equation}
+
+The *Ip* is defined with respec to mass center in Bladed whereas it is defined at elastic center in HAWC2. <br>
+
+\begin{equation}
+Ip^{ea} = Ip^{cg} + m \times (xyz^{cg} - xyz^{ea})^2
+\end{equation}
+
+**BE CAREFUL !!!** -> do not forget to transform inertia results from Bladed coordinate system to HAWC2 coordinate system.
+