Restructures directories; adds setup scripts for python environment and download information

README.md

 # Cloudsat Calipso heating rates
 
 Collection of scripts and figures for cloud-radiative heating rates derived from satellite observations.
+
+To download the CloudSat/Calipso heating rates of 2B-FLXHR-LIDAR via sftp, first follow the instructions at
+[https://www.cloudsat.cira.colostate.edu/order/sftp-access](https://www.cloudsat.cira.colostate.edu/order/sftp-access) to upload your ssh key and the IP address
+of the machine that you use for download. I found that to download the data using IMG Jet, I need to use SRVX1 as a jump server (maybe because of some UNIVIE-IMG firewall?):
+
+``sftp -r -i ~/.ssh/id_rsa_cloudsat -J avoigt@srvx1.img.univie.ac.at aiko.voigtATunivie.ac.at@www.cloudsat.cira.colostate.edu:Data/2B-FLXHR-LIDAR.P2_R05/* .``
+
+``~/.ssh/id_rsa_cloudsat`` is the private key that I generated on SRVX1 and made available on both SRVX1 and Jet. Note that I submitted both the SRVX1 and the JEt ssh-keys and IP addresses
+to the Cloudsat website.
+
+
+Information on the dataset is available
+at [https://www.cloudsat.cira.colostate.edu/data-products/2b-flxhr-lidar](https://www.cloudsat.cira.colostate.edu/data-products/2b-flxhr-lidar).
+
+To read in and work with the HDF4 files, it is helpful to create a dedicated python environment. On Jet, this can be done using micromamba. See the directory ``pythonenv``.
+
+**Directory structure**
+
+* ethz: plots of cloud-radiative heating for a tropical cyclone
+* pythonenv: create dedicated python environment
+

pythonenv/env.txt

+name: cloudsat-calipso
+channels:
+- https://conda.anaconda.org/conda-forge
+dependencies:
+- poppler=24.03.0=h590f24d_0
+- proj=9.3.1=h1d62c97_0
+- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+- rioxarray=0.15.1=pyhd8ed1ab_0
+- libcups=2.3.3=h4637d8d_4
+- libopenblas=0.3.26=pthreads_h413a1c8_0
+- libarchive=3.7.2=h2aa1ff5_1
+- six=1.16.0=pyh6c4a22f_0
+- kealib=1.5.3=h2f55d51_0
+- distributed=2024.3.1=pyhd8ed1ab_0
+- python=3.12.2=hab00c5b_0_cpython
+- aws-c-s3=0.5.3=h4893938_0
+- libclang13=18.1.2=default_h5d6823c_1
+- libgfortran-ng=13.2.0=h69a702a_5
+- lcms2=2.16=hb7c19ff_0
+- libnetcdf=4.9.2=nompi_h9612171_113
+- libabseil=20240116.1=cxx17_h59595ed_2
+- shapely=2.0.3=py312h9e6bd2c_0
+- libthrift=0.19.0=hb90f79a_1
+- certifi=2024.2.2=pyhd8ed1ab_0
+- aws-c-sdkutils=0.1.15=h4466546_2
+- mysql-common=8.3.0=hf1915f5_4
+- openssl=3.2.1=hd590300_1
+- readline=8.2=h8228510_1
+- lz4-c=1.9.4=hcb278e6_0
+- harfbuzz=8.3.0=h3d44ed6_0
+- llvmlite=0.42.0=py312hb06c811_1
+- gstreamer=1.22.9=h98fc4e7_1
+- pthread-stubs=0.4=h36c2ea0_1001
+- fonttools=4.50.0=py312h98912ed_0
+- libuuid=2.38.1=h0b41bf4_0
+- libvorbis=1.3.7=h9c3ff4c_0
+- pyproj=3.6.1=py312h38f1c37_5
+- xcb-util-image=0.4.0=h8ee46fc_1
+- libparquet=15.0.2=h352af49_1_cpu
+- mpg123=1.32.4=h59595ed_0
+- libgcrypt=1.10.3=hd590300_0
+- geos=3.12.1=h59595ed_0
+- libxml2=2.12.6=h232c23b_1
+- brotli=1.1.0=hd590300_1
+- rdma-core=50.0=hd3aeb46_1
+- font-ttf-ubuntu=0.83=h77eed37_1
+- uriparser=0.9.7=h59595ed_1
+- numpy=1.26.4=py312heda63a1_0
+- fasteners=0.17.3=pyhd8ed1ab_0
+- tornado=6.4=py312h98912ed_0
+- libstdcxx-ng=13.2.0=h7e041cc_5
+- _openmp_mutex=4.5=2_gnu
+- pysocks=1.7.1=pyha2e5f31_6
+- libffi=3.4.2=h7f98852_5
+- urllib3=2.2.1=pyhd8ed1ab_0
+- dask-core=2024.3.1=pyhd8ed1ab_0
+- libxcrypt=4.4.36=hd590300_1
+- xorg-libice=1.1.1=hd590300_0
+- libarrow=15.0.2=hb86450c_1_cpu
+- rasterio=1.3.9=py312h26ef92c_2
+- bokeh=3.4.0=pyhd8ed1ab_0
+- numba=0.59.0=py312hacefee8_1
+- libsystemd0=255=h3516f8a_1
+- orc=2.0.0=h1e5e2c1_0
+- libprotobuf=4.25.3=h08a7969_0
+- azure-storage-blobs-cpp=12.10.0=h00ab1b0_1
+- libboost-headers=1.84.0=ha770c72_2
+- ucx=1.15.0=h11edf95_7
+- pyqt=5.15.9=py312h949fe66_5
+- libzlib=1.2.13=hd590300_5
+- libssh2=1.11.0=h0841786_0
+- ncurses=6.4.20240210=h59595ed_0
+- libarrow-gandiva=15.0.2=hb016d2e_1_cpu
+- xorg-xproto=7.0.31=h7f98852_1007
+- libarrow-substrait=15.0.2=h757c851_1_cpu
+- c-ares=1.27.0=hd590300_0
+- s2n=1.4.8=h06160fa_0
+- snuggs=1.4.7=py_0
+- fmt=10.2.1=h00ab1b0_0
+- toml=0.10.2=pyhd8ed1ab_0
+- click=8.1.7=unix_pyh707e725_0
+- libcblas=3.9.0=21_linux64_openblas
+- libgomp=13.2.0=h807b86a_5
+- glib-tools=2.80.0=hde27a5a_1
+- libedit=3.1.20191231=he28a2e2_2
+- openjpeg=2.5.2=h488ebb8_0
+- icu=73.2=h59595ed_0
+- pcre2=10.43=hcad00b1_0
+- aws-c-auth=0.7.16=haed3651_8
+- re2=2023.09.01=h7f4b329_2
+- xorg-libxdmcp=1.1.3=h7f98852_0
+- aws-c-common=0.9.14=hd590300_0
+- libutf8proc=2.8.0=h166bdaf_0
+- libcurl=8.6.0=hca28451_0
+- libbrotlicommon=1.1.0=hd590300_1
+- xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
+- pillow=10.2.0=py312hf3581a9_0
+- libbrotlidec=1.1.0=hd590300_1
+- libtiff=4.6.0=h1dd3fc0_3
+- libnl=3.9.0=hd590300_0
+- glib=2.80.0=hf2295e7_1
+- azure-core-cpp=1.11.1=h91d86a7_1
+- libcrc32c=1.1.2=h9c3ff4c_0
+- pyparsing=3.1.2=pyhd8ed1ab_0
+- kiwisolver=1.4.5=py312h8572e83_1
+- xorg-libsm=1.2.4=h7391055_0
+- pyarrow=15.0.2=py312h176e3d2_1_cpu
+- tiledb=2.21.1=ha9641ad_1
+- aws-checksums=0.1.18=h4466546_2
+- packaging=24.0=pyhd8ed1ab_0
+- xkeyboard-config=2.41=hd590300_0
+- xorg-libxrender=0.9.11=hd590300_0
+- partd=1.4.1=pyhd8ed1ab_0
+- aws-c-io=0.14.6=h96cd748_2
+- libspatialite=5.1.0=h7bd4643_4
+- keyutils=1.6.1=h166bdaf_0
+- font-ttf-inconsolata=3.000=h77eed37_0
+- gflags=2.2.2=he1b5a44_1004
+- lz4=4.3.3=py312h03f37cb_0
+- libgoogle-cloud=2.22.0=h9be4e54_1
+- libbrotlienc=1.1.0=hd590300_1
+- xorg-libxau=1.0.11=hd590300_0
+- libllvm15=15.0.7=hb3ce162_4
+- pytz=2024.1=pyhd8ed1ab_0
+- psutil=5.9.8=py312h98912ed_0
+- xorg-kbproto=1.0.7=h7f98852_1002
+- aws-sdk-cpp=1.11.267=hb1af6a8_4
+- fsspec=2024.3.1=pyhca7485f_0
+- librttopo=1.1.0=h8917695_15
+- libsndfile=1.2.2=hc60ed4a_1
+- ld_impl_linux-64=2.40=h41732ed_0
+- yaml=0.2.5=h7f98852_2
+- libpq=16.2=h33b98f1_1
+- xcb-util=0.4.0=hd590300_1
+- libev=4.33=hd590300_2
+- _libgcc_mutex=0.1=conda_forge
+- attrs=23.2.0=pyh71513ae_0
+- numcodecs=0.12.1=py312h30efb56_0
+- pandas=2.2.1=py312hfb8ada1_0
+- xorg-renderproto=0.11.1=h7f98852_1002
+- xorg-xextproto=7.3.0=h0b41bf4_1003
+- gst-plugins-base=1.22.9=hfa15dee_1
+- libgcc-ng=13.2.0=h807b86a_5
+- tomli=2.0.1=pyhd8ed1ab_0
+- toolz=0.12.1=pyhd8ed1ab_0
+- libjpeg-turbo=3.0.0=hd590300_1
+- libre2-11=2023.09.01=h5a48ba9_2
+- matplotlib-base=3.8.3=py312he5832f3_0
+- cloudpickle=3.0.0=pyhd8ed1ab_0
+- libpng=1.6.43=h2797004_0
+- dask-expr=1.0.5=pyhd8ed1ab_0
+- pyarrow-hotfix=0.6=pyhd8ed1ab_0
+- cligj=0.7.2=pyhd8ed1ab_1
+- pyqt5-sip=12.12.2=py312h30efb56_5
+- libarrow-dataset=15.0.2=h59595ed_1_cpu
+- libflac=1.4.3=h59595ed_0
+- jinja2=3.1.3=pyhd8ed1ab_0
+- mysql-libs=8.3.0=hca2cd23_4
+- libgoogle-cloud-storage=2.22.0=hc7a4891_1
+- expat=2.6.2=h59595ed_0
+- tzcode=2024a=h3f72095_0
+- libiconv=1.17=hd590300_2
+- hdf4=4.2.15=h2a13503_7
+- aws-c-http=0.8.1=hbfc29b2_7
+- setuptools=69.2.0=pyhd8ed1ab_0
+- markupsafe=2.1.5=py312h98912ed_0
+- spdlog=1.12.0=hd2e6256_2
+- geotiff=1.7.1=h6b2125f_15
+- locket=1.0.0=pyhd8ed1ab_0
+- fonts-conda-forge=1=0
+- pip=24.0=pyhd8ed1ab_0
+- aws-c-event-stream=0.4.2=he635cd5_6
+- cytoolz=0.12.3=py312h98912ed_0
+- brotli-python=1.1.0=py312h30efb56_1
+- krb5=1.21.2=h659d440_0
+- ply=3.11=py_1
+- snappy=1.1.10=h9fff704_0
+- libcap=2.69=h0f662aa_0
+- libevent=2.1.12=hf998b51_1
+- libarrow-acero=15.0.2=h59595ed_1_cpu
+- xerces-c=3.2.5=hac6953d_0
+- minizip=4.0.5=h0ab5242_0
+- cftime=1.6.3=py312hc7c0aa3_0
+- libopus=1.3.1=h7f98852_1
+- libwebp-base=1.3.2=hd590300_0
+- click-plugins=1.1.1=py_0
+- alsa-lib=1.2.11=hd590300_1
+- nspr=4.35=h27087fc_0
+- xarray=2024.2.0=pyhd8ed1ab_0
+- libgdal=3.8.4=h7c88fdf_5
+- bzip2=1.0.8=hd590300_5
+- libclang-cpp15=15.0.7=default_h127d8a8_5
+- ca-certificates=2024.2.2=hbcca054_0
+- freexl=2.0.0=h743c826_0
+- pyshp=2.3.1=pyhd8ed1ab_0
+- libllvm18=18.1.2=h2448989_0
+- hdf5=1.14.3=nompi_h4f84152_100
+- glog=0.7.0=hed5481d_0
+- libxkbcommon=1.7.0=h662e7e4_0
+- cartopy=0.22.0=py312hfb8ada1_1
+- libllvm14=14.0.6=hcd5def8_4
+- libxcb=1.15=h0b41bf4_0
+- libexpat=2.6.2=h59595ed_0
+- pyyaml=6.0.1=py312h98912ed_1
+- font-ttf-source-code-pro=2.038=h77eed37_0
+- attr=2.5.1=h166bdaf_1
+- sortedcontainers=2.4.0=pyhd8ed1ab_0
+- cairo=1.18.0=h3faef2a_0
+- tk=8.6.13=noxft_h4845f30_101
+- xz=5.2.6=h166bdaf_0
+- scipy=1.12.0=py312heda63a1_2
+- matplotlib=3.8.3=py312h7900ff3_0
+- libdeflate=1.20=hd590300_0
+- zipp=3.17.0=pyhd8ed1ab_0
+- dbus=1.13.6=h5008d03_3
+- zict=3.0.0=pyhd8ed1ab_0
+- xcb-util-renderutil=0.3.9=hd590300_1
+- zstd=1.5.5=hfc55251_0
+- asciitree=0.3.3=py_2
+- lzo=2.10=h516909a_1000
+- qt-main=5.15.8=h112747c_20
+- xorg-libxext=1.3.4=h0b41bf4_2
+- poppler-data=0.4.12=hd8ed1ab_0
+- libgpg-error=1.48=h71f35ed_0
+- cfitsio=4.4.0=hbdc6101_0
+- libgrpc=1.62.1=h15f2491_0
+- xcb-util-keysyms=0.4.0=h8ee46fc_1
+- zlib=1.2.13=hd590300_5
+- libzip=1.10.1=h2629f0a_3
+- nss=3.98=h1d7d5a4_0
+- libgfortran5=13.2.0=ha4646dd_5
+- zarr=2.17.1=pyhd8ed1ab_0
+- xorg-libx11=1.8.7=h8ee46fc_0
+- postgresql=16.2=h82ecc9d_1
+- dask=2024.3.1=pyhd8ed1ab_0
+- liblapack=3.9.0=21_linux64_openblas
+- graphite2=1.3.13=h58526e2_1001
+- xcb-util-wm=0.4.1=h8ee46fc_1
+- aws-c-mqtt=0.10.3=hffff1cc_2
+- libnsl=2.0.1=hd590300_0
+- blosc=1.21.5=h0f2a231_0
+- libblas=3.9.0=21_linux64_openblas
+- netcdf4=1.6.5=nompi_py312h26027e0_100
+- tzdata=2024a=h0c530f3_0
+- pixman=0.43.2=h59595ed_0
+- munkres=1.1.4=pyh9f0ad1d_0
+- libogg=1.3.4=h7f98852_1
+- aws-crt-cpp=0.26.4=h335f1a1_1
+- libkml=1.3.0=h01aab08_1018
+- json-c=0.17=h7ab15ed_0
+- importlib-metadata=7.1.0=pyha770c72_0
+- freetype=2.12.1=h267a509_2
+- importlib_metadata=7.1.0=hd8ed1ab_0
+- aws-c-compression=0.2.18=h4466546_2
+- azure-storage-common-cpp=12.5.0=h94269e2_4
+- libarrow-flight-sql=15.0.2=h757c851_1_cpu
+- sip=6.7.12=py312h30efb56_0
+- cycler=0.12.1=pyhd8ed1ab_0
+- pyhdf=0.11.3=py312had763d5_2
+- wheel=0.43.0=pyhd8ed1ab_0
+- libarrow-flight=15.0.2=hc6145d9_1_cpu
+- brotli-bin=1.1.0=hd590300_1
+- contourpy=1.2.0=py312h8572e83_0
+- aws-c-cal=0.6.10=ha9bf9b1_2
+- gettext=0.21.1=h27087fc_0
+- python_abi=3.12=4_cp312
+- fontconfig=2.14.2=h14ed4e7_0
+- libaec=1.1.3=h59595ed_0
+- libsqlite=3.45.2=h2797004_0
+- lame=3.100=h166bdaf_1003
+- python-tzdata=2024.1=pyhd8ed1ab_0
+- tblib=3.0.0=pyhd8ed1ab_0
+- libllvm16=16.0.6=hb3ce162_3
+- libnghttp2=1.58.0=h47da74e_1
+- libglib=2.80.0=hf2295e7_1
+- affine=2.4.0=pyhd8ed1ab_0
+- xyzservices=2023.10.1=pyhd8ed1ab_0
+- pulseaudio-client=17.0=hb77b528_0
+- fonts-conda-ecosystem=1=0
+- lerc=4.0.0=h27087fc_0
+- python-dateutil=2.9.0=pyhd8ed1ab_0
+- msgpack-python=1.0.7=py312h8572e83_0
+- giflib=5.2.1=h0b41bf4_3
+- sqlite=3.45.2=h2c6b66d_0
+

pythonenv/setup-pythonenv.sh

+# create environment on IMG Jet using micromamba
+
+module load micromamba
+micromamba create -n cloudsat-calipso
+micromamba install -c conda-forge -n cloudsat-calipso xarray \ rioxarray \ numpy \ matplotlib \ cartopy \ pyhdf \ netcdf4
+micromamba install -c conda-forge -n cloudsat-calipso dask \ zarr \ numba
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