search

nmt28 / C-SHELPh

Apache License 2.0
11 stars 6 forks source link

Error creating Transformer from CRS #11

Closed slyoung20 closed 1 year ago

slyoung20 commented 1 year ago

Hi,

I'm receiving an error that states: Error creating Transformer from CRS My epsg number is 32651. I'm not sure what line of code is in error.

Thank you, Sherry Young

nmt28 commented 1 year ago

Hi,

Can you paste the full error?

what system are you using? Mac OS? Windows? Linux?

Can you let me know what h5 file you are using?

slyoung20 commented 1 year ago

Good evening,

Thank you for your assistance. I really appreciate it. I'm on a windows system. I tried a few different ICESat files including ATL03_20230203162831_06891807_006_01.h5. The error was pertaining to line 17. It could be something I failed to change, I'm not the most experienced programmer. The epsg number output from line 16 is:

epsg number: 32651

ProjError Traceback (most recent call last) Cell In[17], line 2 1 # Orthometrically correct the data using the epsg code ----> 2 lat_utm, lon_utm, photon_h = cshelph.orthometric_correction(latitude, longitude, photon_h, epsg_code)

File ~\cshelph.py:83, in orthometric_correction(lat, lon, Z, epsg) 81 def orthometric_correction(lat, lon, Z, epsg): 82 # transform ellipsod (WGS84) height to orthometric height ---> 83 transformerh = Transformer.from_crs("epsg:4326", "epsg:3855", always_xy=True) 84 X_egm08, Y_egm08, Z_egm08 = transformerh.transform(lon, lat, Z) 86 # transform WGS84 proj to local UTM

File ~\AppData\Roaming\Python\Python310\site-packages\pyproj\transformer.py:625, in Transformer.from_crs(crs_from, crs_to, always_xy, area_of_interest, authority, accuracy, allow_ballpark, force_over, only_best) 552 @staticmethod 553 def from_crs( 554 crs_from: Any, (...) 562 only_best: Optional[bool] = None, 563 ) -> "Transformer": 564 """Make a Transformer from a :obj:pyproj.crs.CRS or input used to create one. 565 566 See: (...) 623 624 """ --> 625 return Transformer( 626 TransformerFromCRS( 627 cstrencode(CRS.from_user_input(crs_from).srs), 628 cstrencode(CRS.from_user_input(crs_to).srs), 629 always_xy=always_xy, 630 area_of_interest=area_of_interest, 631 authority=authority, 632 accuracy=accuracy if accuracy is None else str(accuracy), 633 allow_ballpark=allow_ballpark, 634 force_over=force_over, 635 only_best=only_best, 636 ) 637 )

File ~\AppData\Roaming\Python\Python310\site-packages\pyproj\transformer.py:337, in Transformer.init(self, transformer_maker) 331 raise ProjError( 332 "Transformer must be initialized using: " 333 "'from_crs' or 'from_pipeline'." 334 ) 336 self._local = TransformerLocal() --> 337 self._local.transformer = transformer_maker() 338 self._transformer_maker = transformer_maker

File ~\AppData\Roaming\Python\Python310\site-packages\pyproj\transformer.py:105, in TransformerFromCRS.call(self) 99 def call(self) -> _Transformer: 100 """ 101 Returns 102 ------- 103 _Transformer 104 """ --> 105 return _Transformer.from_crs( 106 self.crs_from, 107 self.crs_to, 108 always_xy=self.always_xy, 109 area_of_interest=self.area_of_interest, 110 authority=self.authority, 111 accuracy=self.accuracy, 112 allow_ballpark=self.allow_ballpark, 113 force_over=self.force_over, 114 only_best=self.only_best, 115 )

File ~\AppData\Roaming\Python\Python310\site-packages\pyproj_transformer.pyx:568, in pyproj._transformer._Transformer.from_crs()

File ~\AppData\Roaming\Python\Python310\site-packages\pyproj_transformer.pyx:344, in pyproj._transformer.proj_create_crs_to_crs()

ProjError: Error creating Transformer from CRS.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Monday, June 19, 2023 5:05 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

Hi,

Can you paste the full error?

what system are you using? Mac OS? Windows? Linux?

Can you let me know what h5 file you are using?

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1597762364, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQICICXINTN5HF26AVNTXMC5JFANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

Thanks I will look into this. Were you able to install all the required packages?

conda install -c conda-forge geopandas utm numpy matplotlib s3fs xarray zarr pyproj proj-data h5py earthaccess h5netcdf dask

pip install cshelph

slyoung20 commented 1 year ago

I was using a jupyter notebook. I installed each separately. When I tried that line of code in a terminal it wouldn't load.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Monday, June 19, 2023 5:21 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

Thanks I will look into this. Were you able to install all the required packages?

conda install -c conda-forge geopandas utm numpy matplotlib s3fs xarray zarr pyproj proj-data h5py earthaccess h5netcdf dask

pip install cshelph

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1597779498, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIGMQYU6TT6QGQJV6STXMC7FDANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

ok, I found your h5 file and works ok on my end, so this is likely a system or package issue.

Can you run:

!conda list

in your notebook and let me know the output?

slyoung20 commented 1 year ago

I started running "conda install -c conda-forge geopandas utm numpy matplotlib s3fs xarray zarr pyproj proj-data h5py earthaccess h5netcdf dask" again, and it's still running. I'll let you know once that is finished if it solves the problem. Thank you for your help. When using the jupyter notebook run_bathymetry_extraction.ipynbhttp://localhost:8890/notebooks/run_bathymetry_extraction.ipynb I should only have to change the file name to try the first run correct?

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Monday, June 19, 2023 6:31 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

ok, I found your h5 file and works ok on my end, so this is likely a system or package issue.

Can you run:

!conda list

and let me know the output?

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1597840136, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIB5ZKSGNVHOGZKMWJLXMDHLNANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

Yes, only the input filename should need to be changed. I did take a quick look at your data. You may need to use the start_lat and end_lat parameters to zoom into your specific area, but we can come on to that later.

For now, I suspect that it's either pyproj or proj-data that is causing the issue. You may need to set specific versions in the installation. Let me know when you can run conda list

slyoung20 commented 1 year ago

Hi,

That was able to install and I was able to run conda list. Conda list is shown below:

packages in environment at C:\ProgramData\anaconda3:

#

Name Version Build Channel

abseil-cpp 20211102.0 h0e60522_0 conda-forge aiobotocore 2.5.0 pyhd8ed1ab_0 conda-forge aiohttp 3.8.4 py310h8d17308_1 conda-forge aioitertools 0.11.0 pyhd8ed1ab_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge anaconda-client 1.11.2 py310haa95532_0 anaconda-navigator 2.4.1 py310haa95532_0 anaconda-project 0.11.1 py310haa95532_0 anyio 3.5.0 py310haa95532_0 argon2-cffi 21.3.0 pyhd3eb1b0_0 argon2-cffi-bindings 21.2.0 py310h2bbff1b_0 arrow-cpp 11.0.0 py310h7cee713_0 asciitree 0.3.3 py_2 conda-forge asttokens 2.0.5 pyhd3eb1b0_0 async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge attrs 22.1.0 py310haa95532_0 aws-c-common 0.4.57 ha925a31_1 aws-c-event-stream 0.1.6 hd77b12b_5 aws-checksums 0.1.9 ha925a31_0 aws-sdk-cpp 1.8.185 hd77b12b_0 backcall 0.2.0 pyhd3eb1b0_0 backports 1.1 pyhd3eb1b0_0 backports.functools_lru_cache 1.6.4 pyhd3eb1b0_0 backports.tempfile 1.0 pyhd3eb1b0_1 backports.weakref 1.0.post1 py_1 beautifulsoup4 4.12.2 py310haa95532_0 blas 1.0 mkl bleach 4.1.0 pyhd3eb1b0_0 blosc 1.21.4 hdccc3a2_0 conda-forge bokeh 3.1.1 pyhd8ed1ab_0 conda-forge boltons 23.0.0 py310haa95532_0 boost-cpp 1.78.0 h9f4b32c_3 conda-forge botocore 1.29.76 pyhd8ed1ab_0 conda-forge bounded-pool-executor 0.0.3 pyhd8ed1ab_0 conda-forge branca 0.6.0 pyhd8ed1ab_0 conda-forge brotli 1.0.9 hcfcfb64_8 conda-forge brotli-bin 1.0.9 hcfcfb64_8 conda-forge brotlipy 0.7.0 py310h2bbff1b_1002 bzip2 1.0.8 he774522_0 c-ares 1.19.1 hcfcfb64_0 conda-forge ca-certificates 2023.5.7 h56e8100_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 hd694305_1014 conda-forge certifi 2023.5.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h2bbff1b_3 cfitsio 4.2.0 h9ebe7e4_0 conda-forge chardet 4.0.0 py310haa95532_1003 charset-normalizer 2.0.4 pyhd3eb1b0_0 click 8.0.4 py310haa95532_0 click-plugins 1.1.1 py_0 conda-forge cligj 0.7.2 pyhd8ed1ab_1 conda-forge cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge clyent 1.2.2 py310haa95532_1 colorama 0.4.6 py310haa95532_0 comm 0.1.2 py310haa95532_0 conda 23.5.0 py310h5588dad_1 conda-forge conda-build 3.24.0 py310haa95532_0 conda-content-trust 0.1.3 py310haa95532_0 conda-pack 0.6.0 pyhd3eb1b0_0 conda-package-handling 2.0.2 py310haa95532_0 conda-package-streaming 0.7.0 py310haa95532_0 conda-repo-cli 1.0.41 py310haa95532_0 conda-token 0.4.0 pyhd3eb1b0_0 conda-verify 3.4.2 py_1 console_shortcut 0.1.1 4 contourpy 1.1.0 py310h232114e_0 conda-forge cryptography 39.0.1 py310h21b164f_0 curl 7.86.0 heaf79c2_1 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge cytoolz 0.12.0 py310h8d17308_1 conda-forge dash 2.10.2 pyhd8ed1ab_0 conda-forge dask 2023.6.0 pyhd8ed1ab_0 conda-forge dask-core 2023.6.0 pyhd8ed1ab_0 conda-forge debugpy 1.5.1 py310hd77b12b_0 decorator 5.1.1 pyhd3eb1b0_0 defusedxml 0.7.1 pyhd3eb1b0_0 distributed 2023.6.0 pyhd8ed1ab_0 conda-forge earthaccess 0.5.2 pyhd8ed1ab_0 conda-forge entrypoints 0.4 py310haa95532_0 executing 0.8.3 pyhd3eb1b0_0 expat 2.5.0 h63175ca_1 conda-forge fasteners 0.17.3 pyhd8ed1ab_0 conda-forge filelock 3.9.0 py310haa95532_0 fiona 1.8.22 py310h30f9a14_2 conda-forge flask 2.2.3 pyhd8ed1ab_0 conda-forge folium 0.14.0 pyhd8ed1ab_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.2 hbde0cde_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.40.0 py310h8d17308_0 conda-forge freetype 2.12.1 ha860e81_0 freexl 1.0.6 h67ca5e6_1 conda-forge frozenlist 1.3.3 py310h8d17308_0 conda-forge fsspec 2023.6.0 pyh1a96a4e_0 conda-forge future 0.18.3 py310haa95532_0 gdal 3.5.3 py310h198874d_5 conda-forge geopandas 0.13.2 pyhd8ed1ab_1 conda-forge geopandas-base 0.13.2 pyha770c72_1 conda-forge geos 3.11.1 h1537add_0 conda-forge geotiff 1.7.1 h4ffd875_4 conda-forge gettext 0.21.1 h5728263_0 conda-forge gflags 2.2.2 ha925a31_1004 conda-forge giflib 5.2.1 h8cc25b3_3 glib 2.76.3 h12be248_0 conda-forge glib-tools 2.76.3 h12be248_0 conda-forge glob2 0.7 pyhd3eb1b0_0 glog 0.5.0 h4797de2_0 conda-forge gst-plugins-base 1.20.3 h001b923_2 conda-forge gstreamer 1.20.3 h6b5321d_2 conda-forge h5netcdf 1.2.0 pyhd8ed1ab_0 conda-forge h5py 3.8.0 nompi_py310hae7a582_100 conda-forge hdf4 4.2.15 h1b1b6ef_5 conda-forge hdf5 1.12.2 nompi_h2a0e4a3_100 conda-forge icc_rt 2022.1.0 h6049295_2 icu 70.1 h0e60522_0 conda-forge idna 3.4 py310haa95532_0 importlib-metadata 6.7.0 pyha770c72_0 conda-forge importlib_metadata 6.7.0 hd8ed1ab_0 conda-forge intel-openmp 2023.1.0 h59b6b97_46319 ipykernel 6.19.2 py310h9909e9c_0 ipython 8.12.0 py310haa95532_0 ipython_genutils 0.2.0 pyhd3eb1b0_1 itsdangerous 2.1.2 pyhd8ed1ab_0 conda-forge jedi 0.18.1 py310haa95532_1 jinja2 3.1.2 py310haa95532_0 jmespath 1.0.1 pyhd8ed1ab_0 conda-forge joblib 1.2.0 pyhd8ed1ab_0 conda-forge jpeg 9e h2bbff1b_1 jsonpatch 1.32 pyhd3eb1b0_0 jsonpointer 2.1 pyhd3eb1b0_0 jsonschema 4.17.3 py310haa95532_0 jupyter_client 8.1.0 py310haa95532_0 jupyter_core 5.3.0 py310haa95532_0 jupyter_events 0.6.3 py310haa95532_0 jupyter_server 2.5.0 py310haa95532_0 jupyter_server_terminals 0.4.4 py310haa95532_0 jupyterlab_pygments 0.1.2 py_0 kealib 1.5.0 h61be68b_0 conda-forge kiwisolver 1.4.4 py310h232114e_1 conda-forge krb5 1.19.4 h5b6d351_0 lcms2 2.14 h90d422f_0 conda-forge lerc 3.0 hd77b12b_0 libarchive 3.6.2 h2033e3e_1 libbrotlicommon 1.0.9 hcfcfb64_8 conda-forge libbrotlidec 1.0.9 hcfcfb64_8 conda-forge libbrotlienc 1.0.9 hcfcfb64_8 conda-forge libclang 14.0.6 default_hb5a9fac_1 libclang13 14.0.6 default_h8e68704_1 libcurl 7.86.0 heaf79c2_1 conda-forge libdeflate 1.17 h2bbff1b_0 libexpat 2.5.0 h63175ca_1 conda-forge libffi 3.4.4 hd77b12b_0 libgdal 3.5.3 hc3442b3_5 conda-forge libglib 2.76.3 he8f3873_0 conda-forge libiconv 1.17 h8ffe710_0 conda-forge libkml 1.3.0 hf2ab4e4_1015 conda-forge liblief 0.12.3 hd77b12b_0 libnetcdf 4.8.1 nompi_h8c042bf_106 conda-forge libogg 1.3.5 h2bbff1b_1 libpng 1.6.39 h8cc25b3_0 libpq 15.1 h04fd8be_1 conda-forge libprotobuf 3.20.3 h12be248_0 conda-forge librttopo 1.1.0 he22b5cd_12 conda-forge libsodium 1.0.18 h62dcd97_0 libspatialindex 1.9.3 h39d44d4_4 conda-forge libspatialite 5.0.1 h07bf483_22 conda-forge libsqlite 3.42.0 hcfcfb64_0 conda-forge libssh2 1.10.0 h680486a_3 conda-forge libthrift 0.15.0 h636ae23_1 conda-forge libtiff 4.4.0 h8a3f274_2 libvorbis 1.3.7 he774522_0 libwebp 1.2.4 hbc33d0d_1 libwebp-base 1.2.4 h2bbff1b_1 libxml2 2.10.3 h0ad7f3c_0 libxslt 1.1.37 h2bbff1b_0 libzip 1.9.2 hfed4ece_1 conda-forge libzlib 1.2.13 hcfcfb64_5 conda-forge locket 1.0.0 pyhd8ed1ab_0 conda-forge lxml 4.9.2 py310h2bbff1b_0 lz4 4.3.2 py310hbbb2075_0 conda-forge lz4-c 1.9.4 h2bbff1b_0 m2-msys2-runtime 2.5.0.17080.65c939c 3 m2-patch 2.7.5 2 mapclassify 2.5.0 pyhd8ed1ab_1 conda-forge markupsafe 2.1.1 py310h2bbff1b_0 matplotlib 3.7.1 py310h5588dad_0 conda-forge matplotlib-base 3.7.1 py310h51140c5_0 conda-forge matplotlib-inline 0.1.6 py310haa95532_0 menuinst 1.4.19 py310h59b6b97_0 mistune 0.8.4 py310h2bbff1b_1000 mkl 2023.1.0 h8bd8f75_46356 mkl-service 2.4.0 py310h2bbff1b_1 mkl_fft 1.3.6 py310h4ed8f06_1 mkl_random 1.2.2 py310h4ed8f06_1 msgpack-python 1.0.5 py310h232114e_0 conda-forge msys2-conda-epoch 20160418 1 multidict 6.0.4 py310h8d17308_0 conda-forge multimethod 1.9.1 pyhd8ed1ab_0 conda-forge munch 3.0.0 pyhd8ed1ab_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge navigator-updater 0.4.0 py310haa95532_0 nbclassic 0.5.5 py310haa95532_0 nbclient 0.5.13 py310haa95532_0 nbconvert 6.5.4 py310haa95532_0 nbformat 5.7.0 py310haa95532_0 nest-asyncio 1.5.6 py310haa95532_0 networkx 3.1 pyhd8ed1ab_0 conda-forge notebook 6.5.4 py310haa95532_0 notebook-shim 0.2.2 py310haa95532_0 numcodecs 0.11.0 py310h00ffb61_1 conda-forge numpy 1.24.3 py310h055cbcc_1 numpy-base 1.24.3 py310h65a83cf_1 openjpeg 2.5.0 hc9384bd_1 conda-forge openssl 1.1.1u hcfcfb64_0 conda-forge orc 1.7.4 h623e30f_1 packaging 23.0 py310haa95532_0 pandas 2.0.2 py310h1c4a608_0 conda-forge pandocfilters 1.5.0 pyhd3eb1b0_0 parso 0.8.3 pyhd3eb1b0_0 partd 1.4.0 pyhd8ed1ab_0 conda-forge pathlib 1.0.1 pyhd3eb1b0_1 pcre 8.45 hd77b12b_0 pcre2 10.40 h17e33f8_0 conda-forge pickleshare 0.7.5 pyhd3eb1b0_1003 pillow 9.4.0 py310hd77b12b_0 pip 23.1.2 pypi_0 pypi pixman 0.40.0 h8ffe710_0 conda-forge pkginfo 1.9.6 py310haa95532_0 platformdirs 2.5.2 py310haa95532_0 plotly 5.15.0 pyhd8ed1ab_0 conda-forge pluggy 1.0.0 py310haa95532_1 ply 3.11 py310haa95532_0 pooch 1.7.0 pyha770c72_3 conda-forge poppler 22.11.0 ha6c1112_0 conda-forge poppler-data 0.4.12 hd8ed1ab_0 conda-forge postgresql 15.1 h392df6f_1 conda-forge powershell_shortcut 0.0.1 3 pqdm 0.2.0 pyhd8ed1ab_0 conda-forge proj 9.1.0 h3863b3b_0 conda-forge proj-data 1.14 hd8ed1ab_0 conda-forge prometheus_client 0.14.1 py310haa95532_0 prompt-toolkit 3.0.36 py310haa95532_0 psutil 5.9.0 py310h2bbff1b_0 pure_eval 0.2.2 pyhd3eb1b0_0 py-lief 0.12.3 py310hd77b12b_0 pyarrow 11.0.0 py310h790e06d_0 pycosat 0.6.4 py310h2bbff1b_0 pycparser 2.21 pyhd3eb1b0_0 pygments 2.15.1 py310haa95532_1 pyjwt 2.4.0 py310haa95532_0 pyopenssl 23.0.0 py310haa95532_0 pyparsing 3.1.0 pyhd8ed1ab_0 conda-forge pyproj 3.4.1 py310h0e9dbc5_0 conda-forge pyqt 5.15.7 py310hd77b12b_0 pyqt5-sip 12.11.0 py310hd77b12b_0 pyrsistent 0.18.0 py310h2bbff1b_0 pysocks 1.7.1 py310haa95532_0 python 3.10.9 h966fe2a_1 python-cmr 0.7.0 pyhd8ed1ab_0 conda-forge python-dateutil 2.8.2 pyhd3eb1b0_0 python-fastjsonschema 2.16.2 py310haa95532_0 python-json-logger 2.0.7 py310haa95532_0 python-libarchive-c 2.9 pyhd3eb1b0_1 python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 2_cp310 conda-forge pytz 2022.7 py310haa95532_0 pywin32 305 py310h2bbff1b_0 pywinpty 2.0.10 py310h5da7b33_0 pyyaml 6.0 py310h2bbff1b_1 pyzmq 25.1.0 py310hd77b12b_0 qt-main 5.15.6 hf0cf448_0 conda-forge qt-webengine 5.15.9 hb9a9bb5_5 qtpy 2.2.0 py310haa95532_0 qtwebkit 5.212 h992fabe_7 conda-forge re2 2022.04.01 h0e60522_0 conda-forge requests 2.29.0 py310haa95532_0 requests-toolbelt 0.9.1 pyhd3eb1b0_0 rfc3339-validator 0.1.4 py310haa95532_0 rfc3986-validator 0.1.1 py310haa95532_0 rtree 1.0.1 py310h1cbd46b_1 conda-forge ruamel.yaml 0.17.21 py310h2bbff1b_0 ruamel.yaml.clib 0.2.6 py310h2bbff1b_1 ruamel_yaml 0.17.21 py310h2bbff1b_0 s3fs 2023.6.0 pyhd8ed1ab_0 conda-forge scikit-learn 1.2.2 py310hd266714_2 conda-forge scipy 1.10.1 py310h309d312_1 send2trash 1.8.0 pyhd3eb1b0_1 setuptools 65.6.3 py310haa95532_0 shapely 2.0.1 py310h8c82734_0 conda-forge sip 6.6.2 py310hd77b12b_0 six 1.16.0 pyhd3eb1b0_1 snappy 1.1.10 hfb803bf_0 conda-forge sniffio 1.2.0 py310haa95532_1 sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge soupsieve 2.4 py310haa95532_0 sqlite 3.41.2 h2bbff1b_0 stack_data 0.2.0 pyhd3eb1b0_0 tbb 2021.8.0 h59b6b97_0 tblib 1.7.0 pyhd8ed1ab_0 conda-forge tenacity 8.2.2 pyhd8ed1ab_0 conda-forge terminado 0.17.1 py310haa95532_0 threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge tiledb 2.11.3 h5689973_1 conda-forge tinycss2 1.2.1 py310haa95532_0 tinynetrc 1.3.1 pyhd8ed1ab_0 conda-forge tk 8.6.12 h2bbff1b_0 toml 0.10.2 pyhd3eb1b0_0 tomli 2.0.1 py310haa95532_0 toolz 0.12.0 py310haa95532_0 tornado 6.2 py310h2bbff1b_0 tqdm 4.65.0 py310h9909e9c_0 traitlets 5.7.1 py310haa95532_0 typing-extensions 4.6.3 py310haa95532_0 typing_extensions 4.6.3 py310haa95532_0 tzdata 2023c h04d1e81_0 ucrt 10.0.22621.0 h57928b3_0 conda-forge ujson 5.4.0 py310hd77b12b_0 unicodedata2 15.0.0 py310h8d17308_0 conda-forge urllib3 1.26.16 py310haa95532_0 utf8proc 2.6.1 h2bbff1b_0 utm 0.7.0 pyhd8ed1ab_0 conda-forge vc 14.2 h21ff451_1 vc14_runtime 14.34.31931 h5081d32_16 conda-forge vs2015_runtime 14.34.31931 hed1258a_16 conda-forge wcwidth 0.2.5 pyhd3eb1b0_0 webencodings 0.5.1 py310haa95532_1 websocket-client 0.58.0 py310haa95532_4 werkzeug 2.3.6 pyhd8ed1ab_0 conda-forge wheel 0.38.4 py310haa95532_0 win_inet_pton 1.1.0 py310haa95532_0 wincertstore 0.2 py310haa95532_2 winpty 0.4.3 4 wrapt 1.15.0 py310h8d17308_0 conda-forge xarray 2023.5.0 pyhd8ed1ab_0 conda-forge xerces-c 3.2.4 h63175ca_2 conda-forge xyzservices 2023.5.0 pyhd8ed1ab_1 conda-forge xz 5.4.2 h8cc25b3_0 yaml 0.2.5 he774522_0 yarl 1.9.2 py310h8d17308_0 conda-forge zarr 2.15.0 pyhd8ed1ab_0 conda-forge zeromq 4.3.4 hd77b12b_0 zict 3.0.0 pyhd8ed1ab_0 conda-forge zipp 3.15.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hcfcfb64_5 conda-forge zstandard 0.19.0 py310h2bbff1b_0 zstd 1.5.5 hd43e919_0

Note: you may need to restart the kernel to use updated packages.

I restarted the kernel and tried to run again. Now I'm getting an error on Matplotlib.

ImportError Traceback (most recent call last) Cell In[1], line 3 1 import numpy as np 2 import h5py as h5 ----> 3 import matplotlib.pyplot as plt 4 import pyproj 5 from pyproj import Proj

File ~\AppData\Roaming\Python\Python310\site-packages\matplotlib__init__.py:148 144 from packaging.version import parse as parse_version 146 # cbook must import matplotlib only within function 147 # definitions, so it is safe to import from it here. --> 148 from . import _api, _version, cbook, _docstring, rcsetup 149 from matplotlib.cbook import sanitize_sequence 150 from matplotlib._api import MatplotlibDeprecationWarning

File ~\AppData\Roaming\Python\Python310\site-packages\matplotlib\rcsetup.py:27 25 from matplotlib import _api, cbook 26 from matplotlib.cbook import ls_mapper ---> 27 from matplotlib.colors import Colormap, is_color_like 28 from matplotlib._fontconfig_pattern import parse_fontconfig_pattern 29 from matplotlib._enums import JoinStyle, CapStyle

File ~\AppData\Roaming\Python\Python310\site-packages\matplotlib\colors.py:51 49 from numbers import Number 50 import re ---> 51 from PIL import Image 52 from PIL.PngImagePlugin import PngInfo 54 import matplotlib as mpl

File C:\ProgramData\anaconda3\lib\site-packages\PIL\Image.py:103 94 MAX_IMAGE_PIXELS = int(1024 1024 1024 // 4 // 3) 97 try: 98 # If the _imaging C module is not present, Pillow will not load. 99 # Note that other modules should not refer to _imaging directly; 100 # import Image and use the Image.core variable instead. 101 # Also note that Image.core is not a publicly documented interface, 102 # and should be considered private and subject to change. --> 103 from . import _imaging as core 105 if version != getattr(core, "PILLOW_VERSION", None): 106 msg = ( 107 "The _imaging extension was built for another version of Pillow or PIL:\n" 108 f"Core version: {getattr(core, 'PILLOW_VERSION', None)}\n" 109 f"Pillow version: {version}" 110 )

ImportError: DLL load failed while importing _imaging: The specified module could not be found.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Monday, June 19, 2023 6:41 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

Yes, only the input filename should need to be changed. I did take a quick look at your data. You may need to use the start_lat and end_lat parameters to zoom into your specific area, but we can come on to that later.

For now, I suspect that it's either pyproj or proj-data that is causing the issue. You may need to set specific versions in the installation. Let me know when you can run conda list

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1597845123, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIE6XSRZT4YDA4OFEWDXMDIS7ANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

ok, so this is a very busy environment so it's likely that there are competing packages and conflicts that are causing you issues.

Lets begin by creating a new clean environment:

conda create -n bathy python=3.10

This will create a new environment for you called "bathy". Then start this environment:

conda activate bathy

Then install mamba. This is like conda but much faster:

conda install -c Conda-forge mamba

Then install the packages we need:

mamba install -c conda-forge geopandas utm numpy matplotlib s3fs xarray zarr pyproj proj-data h5py earthaccess h5netcdf dask tqdm

Then:

pip install cshelph

In your notebook try and import the required packages and see if we can get that far

slyoung20 commented 1 year ago

Good morning Dr. Thomas,

Thank you for your help. It appears that there is some issue still with imaging in the Pillow plugin in Jupyter. When checking in a python terminal it says: Requirement already satisfied: Pillow in c:\users\18042\appdata\local\packages\pythonsoftwarefoundation.python.3.11_qbz5n2kfra8p0\localcache\local-packages\python311\site-packages (9.5.0) The pillow site here says: https://pillow.readthedocs.io/en/stable/installation.html Pillow and PIL cannot co-exist in the same environment. Before installing Pillow, please uninstall PIL. and Pillow >= 1.0 no longer supports import Image. Please use from PIL import Image instead. and Pillow >= 2.1.0 no longer supports import _imaging. Please use from PIL.Image import core as _imaging instead.

I've tried both of these, and get the following error still.

ImportError Traceback (most recent call last) Cell In[8], line 1 ----> 1 from PIL.Image import core as _imaging

File C:\ProgramData\anaconda3\lib\site-packages\PIL\Image.py:103 94 MAX_IMAGE_PIXELS = int(1024 1024 1024 // 4 // 3) 97 try: 98 # If the _imaging C module is not present, Pillow will not load. 99 # Note that other modules should not refer to _imaging directly; 100 # import Image and use the Image.core variable instead. 101 # Also note that Image.core is not a publicly documented interface, 102 # and should be considered private and subject to change. --> 103 from . import _imaging as core 105 if version != getattr(core, "PILLOW_VERSION", None): 106 msg = ( 107 "The _imaging extension was built for another version of Pillow or PIL:\n" 108 f"Core version: {getattr(core, 'PILLOW_VERSION', None)}\n" 109 f"Pillow version: {version}" 110 )

ImportError: DLL load failed while importing _imaging: The specified module could not be found.

I don't have enough programming experience to figure out how to point to the correct version and remove whatever needs to be removed in Jupyter to get past this error.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Tuesday, June 20, 2023 11:08 AM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

ok, so this is a very busy environment so it's likely that there are competing packages and conflicts that are causing you issues.

Lets begin by creating a new clean environment:

conda create -n bathy python=3.10

This will create a new environment for you called "bathy". Then start this environment:

conda activate bathy

Then install mamba. This is like conda but much faster:

conda install -c Conda-forge mamba

Then install the packages we need:

mamba install -c conda-forge geopandas utm numpy matplotlib s3fs xarray zarr pyproj proj-data h5py earthaccess h5netcdf dask tqdm

Then:

pip install cshelph

In your notebook try and import the required packages and see if we can get that far

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1598980784, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIHTYOHQP42VVLG7RDLXMG4HHANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

Hey, no problem. Environment issues are common but we can get it figured out.

When importing matplotlib are you in the new environment you created? You can access this using:

conda activate Bathy

It is possible that your python notebook environment is not finding the right environment.

When in the new python environment (bathy):

mamba install -c condo-forge ipykernel

After this, restart all of your python terminals and notebooks. You should then be able to do the following when in a notebook and select the Bathy environment:

Screen Shot 2023-06-21 at 8 43 43 PM

Image from: https://stackoverflow.com/questions/47191297/how-to-switch-environment-on-jupyter-notebook-for-new-notebook

As far as I know, we don't need PIL/pillow so lets try and avoid it for now and come back to it if it gives us matplotlib import errors.

Lastly, when in the bath env do:

conda list

and paste the results here. :)

slyoung20 commented 1 year ago

Good afternoon,

It looks like we need to be working with python version less than 3.6, so 3.5 or earlier and pillow version 5.4 or earlier to fix the error I'm receiving with matplotlib. I've tried installing earlier versions of python into the new environment, but Jupyter keeps reverting back to python 3.11 (I just reinstalled navigator on this computer). Is there a way to remove pillow from the code when running it? I couldn't get mamba to install either, so I'm still working with conda. I can't seem to start a new kernel.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Wednesday, June 21, 2023 3:49 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

Hey, no problem. Environment issues are common but we can get it figured out.

When importing matplotlib are you in the new environment you created? You can access this using:

conda activate Bathy

It is possible that your python notebook environment is not finding the right environment.

When in the new python environment (bathy):

mamba install -c condo-forge ipykernel

After this, restart all of your python terminals and notebooks. You should then be able to do the following when in a notebook and select the Bathy environment:

[Screen Shot 2023-06-21 at 8 43 43 PM]https://user-images.githubusercontent.com/22138389/247708773-ca3571c2-5d20-443f-b23a-dec7794ffd1b.png

As far as I know, we don't need PIL/pillow so lets try and avoid it for now and come back to it if it gives us matplotlib import errors.

Lastly, when in the bath env do:

conda list

and paste the results here. :)

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1601577706, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIGVXLMBMRZM4VAUB2TXMNF3VANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

hmmm, python 3. is old now and I am able to run all what I need in python 3.11. It's strange that mamba wouldn't install. Lets try some things step by step. In your base environment (the one that starts when you open anaconda) try:

conda install -n base -c condo-forge mamba

Then lets try making a new env like before (based on 3.10 in anticipation of some 3.11 issues):

conda create -n bathy python=3.10

Confirm that you can make this work by:

conda activate bathy

If you get an error that the environment already exists, try:

conda deactivate

conda remove -n bathy --all

slyoung20 commented 1 year ago

This is what I got:

(base) C:\Users\18042>conda install -n base -c condo-forge mamba Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: HTTP 404 NOT FOUND for channel condo-forge https://conda.anaconda.org/condo-forge

The channel is not accessible or is invalid.

You will need to adjust your conda configuration to proceed. Use conda config --show channels to view your configuration's current state, and use conda config --show-sources to view config file locations.

(base) C:\Users\18042>conda config --show channels channels:

(base) C:\Users\18042>

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Wednesday, June 21, 2023 4:06 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

hmmm, python 3. is old now and I am able to run all what I need in python 3.11. It's strange that mamba wouldn't install. Lets try some things step by step. In your base environment (the one that starts when you open anaconda) try:

conda install -n base -c condo-forge mamba

Then lets try making a new env like before (based on 3.10 in anticipation of some 3.11 issues):

conda create -n bathy python=3.10

Confirm that you can make this work by:

conda activate bathy

If you get an error that the environment already exists, try:

conda deactivate

conda remove -n bathy --all

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1601600875, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIEOXH4MH3TYJKOCHVTXMNH3RANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

ah apologies, conda-forge got corrected to condo-forge. Please try: conda-forge

slyoung20 commented 1 year ago

Yes, I believe that's what I entered. Just tried again.

(base) C:\Users\18042>conda install -n base -c condo-forge mamba Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: HTTP 404 NOT FOUND for channel condo-forge https://conda.anaconda.org/condo-forge

The channel is not accessible or is invalid.

You will need to adjust your conda configuration to proceed. Use conda config --show channels to view your configuration's current state, and use conda config --show-sources to view config file locations.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Wednesday, June 21, 2023 4:13 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

ah apologies, conda-forge got corrected to condo-forge. Please try: condo-forge

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1601609235, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIEC4DYT75SXKY3N4B3XMNIXVANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

looks like you're still passing in condo-forge? Try:

conda install -n base -c conda-forge mamba

slyoung20 commented 1 year ago

Sorry, read that backwards. It's trying to install now. This is what it shows so far, this is what happened before and it never got past this. (base) C:\Users\18042>conda install -n base -c conda-forge mamba Collecting package metadata (current_repodata.json): done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source. Collecting package metadata (repodata.json):

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Wednesday, June 21, 2023 4:23 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

looks like you're still passing in condo-forge? Try:

conda install -n base -c conda-forge mamba

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1601619385, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIDTEBTFBQJYY4E2N53XMNJ3FANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

yes, conda installs can take a while which is why we want to use mamba instead. However, me need to use conda to first install mamba in a strange "chicken and egg" situation

If this takes a huge amount of time, you can try:

conda clean --all

before trying the install again

slyoung20 commented 1 year ago

I cleared it and restarted it, but it still won't go past solving the environment.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Wednesday, June 21, 2023 4:23 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

looks like you're still passing in condo-forge? Try:

conda install -n base -c conda-forge mamba

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1601619385, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIDTEBTFBQJYY4E2N53XMNJ3FANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

slyoung20 commented 1 year ago

Good evening,

I've still gotten nowhere with this. When after I create a new environment, it still has all the packages installed. When I try to update matplotlib in the new environment this is what happens. I'm thinking this could be an issue with the version of navigator?

PS C:\Users\18042> conda update matplotlib Collecting package metadata (current_repodata.json): done Solving environment: \ The environment is inconsistent, please check the package plan carefully The following packages are causing the inconsistency:

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Wednesday, June 21, 2023 4:39 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

yes, conda installs can take a while which is why we want to use mamba instead. However, me need to use conda to first install mamba in a strange "chicken and egg" situation

If this takes a huge amount of time, you can try:

conda clean --all

before trying the install again

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1601639889, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIBAN6BDNDA5N6JHWGTXMNLXFANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

slyoung20 commented 1 year ago

Dr. Thomas,

Got it, finally. Thank you so much for your help. Evidentially, when you do a fresh install on Anaconda Navigator, it asks if you want to update it. If you do, it installs python 11, it will also do this if you try to set up a new environment in the terminal. If you click"y", it adds all new packages which are incompatible with matplotlib. This time, I didn't update and said no. I also didn't use a separate environment, I just started with the import block and I didn't get the matplotlib error. I am getting new errors though, so far it can't read the file because of:

OSError: [Errno 22] Unable to open file (unable to open file: name = 'C:\Users8042\ATL03_20230203162831_06891807_006_01.h5', errno = 22, error message = 'Invalid argument', flags = 0, o_flags = 0)

I'll try to debug that.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Wednesday, June 21, 2023 4:39 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

yes, conda installs can take a while which is why we want to use mamba instead. However, me need to use conda to first install mamba in a strange "chicken and egg" situation

If this takes a huge amount of time, you can try:

conda clean --all

before trying the install again

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1601639889, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIBAN6BDNDA5N6JHWGTXMNLXFANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

It may take a while. I suggest leaving it run for a while. Once mamba is installed, things become much easier

slyoung20 commented 1 year ago

Good afternoon,

So, I got past the part I was stuck on. It seems that if you install any packages or update any, Anaconda updates python to 11 and updates all of the packages at once. This causes a conflict with Matplotlib for some reason. After installing and uninstalling Anaconda 6 times, I was able to get it to run without installing anything or updating any packages. If you run Conda at all, matplotlib is in conflict again and you have to delete everything and reinstall. The error I'm getting now is with the transformation. I'm not sure if it's because our data is already in UTM or not.

ProjError Traceback (most recent call last) Cell In[18], line 2 1 # Orthometrically correct the data using the epsg code ----> 2 lat_utm, lon_utm, photon_h = cshelph.orthometric_correction(latitude, longitude, photon_h, epsg_code)

File ~\C-SHELPh-2.5.0\cshelph\cshelph.py:83, in orthometric_correction(lat, lon, Z, epsg) 81 def orthometric_correction(lat, lon, Z, epsg): 82 # transform ellipsod (WGS84) height to orthometric height ---> 83 transformerh = Transformer.from_crs("epsg:4326", "epsg:3855", always_xy=True) 84 X_egm08, Y_egm08, Z_egm08 = transformerh.transform(lon, lat, Z) 86 # transform WGS84 proj to local UTM

File ~\AppData\Roaming\Python\Python310\site-packages\pyproj\transformer.py:625, in Transformer.from_crs(crs_from, crs_to, always_xy, area_of_interest, authority, accuracy, allow_ballpark, force_over, only_best) 552 @staticmethod 553 def from_crs( 554 crs_from: Any, (...) 562 only_best: Optional[bool] = None, 563 ) -> "Transformer": 564 """Make a Transformer from a :obj:pyproj.crs.CRS or input used to create one. 565 566 See: (...) 623 624 """ --> 625 return Transformer( 626 TransformerFromCRS( 627 cstrencode(CRS.from_user_input(crs_from).srs), 628 cstrencode(CRS.from_user_input(crs_to).srs), 629 always_xy=always_xy, 630 area_of_interest=area_of_interest, 631 authority=authority, 632 accuracy=accuracy if accuracy is None else str(accuracy), 633 allow_ballpark=allow_ballpark, 634 force_over=force_over, 635 only_best=only_best, 636 ) 637 )

File ~\AppData\Roaming\Python\Python310\site-packages\pyproj\transformer.py:337, in Transformer.init(self, transformer_maker) 331 raise ProjError( 332 "Transformer must be initialized using: " 333 "'from_crs' or 'from_pipeline'." 334 ) 336 self._local = TransformerLocal() --> 337 self._local.transformer = transformer_maker() 338 self._transformer_maker = transformer_maker

File ~\AppData\Roaming\Python\Python310\site-packages\pyproj\transformer.py:105, in TransformerFromCRS.call(self) 99 def call(self) -> _Transformer: 100 """ 101 Returns 102 ------- 103 _Transformer 104 """ --> 105 return _Transformer.from_crs( 106 self.crs_from, 107 self.crs_to, 108 always_xy=self.always_xy, 109 area_of_interest=self.area_of_interest, 110 authority=self.authority, 111 accuracy=self.accuracy, 112 allow_ballpark=self.allow_ballpark, 113 force_over=self.force_over, 114 only_best=self.only_best, 115 )

File ~\AppData\Roaming\Python\Python310\site-packages\pyproj_transformer.pyx:568, in pyproj._transformer._Transformer.from_crs()

File ~\AppData\Roaming\Python\Python310\site-packages\pyproj_transformer.pyx:344, in pyproj._transformer.proj_create_crs_to_crs()

ProjError: Error creating Transformer from CRS.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Thursday, June 22, 2023 1:00 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

It may take a while. I suggest leaving it run for a while. Once mamba is installed, things become much easier

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1603015994, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIELSD2J7HD6ZVOG7PDXMR24RANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

ok, so it looks like we have gone full circle here. Do you have a new clean environment using:

conda create -n bathy python=3.10

slyoung20 commented 1 year ago

You can't create an environment; it updates Conda and gives you python 11 which conflicts with matplotlib. For some reason, Anaconda won't let me use Conda, without updating Conda which triggers Anaconda to update everything at once, python included. Then the matplotlib conflict is triggered. It wouldn't allow me to create an environment with a different version of python either, no matter how many times I did it. Finally, I just decided to go with Anaconda as it is with python 10. This works as long as I don't install or update anything.

I think the problem I have now is that my data is already in UTM. When I ran it with your file it worked. I'm going to try to download an IceSat file in WGS and see if that works. Fingers crossed, it should. Doing that now.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Thursday, June 22, 2023 1:41 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

ok, so it looks like we have gone full circle here. Do you have a new clean environment using:

conda create -n bathy python=3.10

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1603070053, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIAF7WJEV3B2YDGD37TXMR7WJANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

slyoung20 commented 1 year ago

Hi Nathan,

I checked one of the files in Arc, it is in WGS1984 projection. The EPSG should be 4326. Not sure why when I run the code I get:

Find the epsg code

epsg_code = cshelph.convert_wgs_to_utm(latitude[0], longitude[0]) epsg_num = int(epsg_code.split(':')[-1]) print(f"epsg number: {epsg_num}")

epsg number: 32651

But when I run your file it works. Do I need to change any inputs that I may be missing? Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Thursday, June 22, 2023 1:41 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

ok, so it looks like we have gone full circle here. Do you have a new clean environment using:

conda create -n bathy python=3.10

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1603070053, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIAF7WJEV3B2YDGD37TXMR7WJANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

slyoung20 commented 1 year ago

Hello Dr. Thomas,

OK, I got this working mostly now, looks like I'm missing one input: surface buffer. There are many, many, conflicts between all of the current packages that have to be resolved one by one. If you get somebody else with this issue, that's the problem. Honestly, I'm not even sure what the final setup is at this point, but it works.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Thursday, June 22, 2023 1:41 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

ok, so it looks like we have gone full circle here. Do you have a new clean environment using:

conda create -n bathy python=3.10

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1603070053, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIAF7WJEV3B2YDGD37TXMR7WJANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

Excellent, thanks for working all of this out. This isn't developed or tested on windows, so there's no guarantee that it can work. One way to check your environment credentials is:

conda list

As for the buffer argument, I updated the code recently so first uninstall cshelph.

pip uninstall cshelph

Then install it again:

pip install cshelph

If the error happens again, let me know and I'll update the code

slyoung20 commented 1 year ago

Hi Nathan,

I got that fixed last night after I emailed you. It looks like you just set the buffer to -0.5 correct? I read that on the github page under your previous responses. I'm getting this error now, everything works until I get here:

print('Fetching water temperature...') water_temp = cshelph.get_water_temp(is2_h5_file, latitude, longitude) print(f"water temp: {water_temp} deg C")

IndexError Traceback (most recent call last) Cell In[20], line 2 1 print('Fetching water temperature...') ----> 2 water_temp = cshelph.get_water_temp(is2_h5_file, latitude, longitude) 3 print(f"water temp: {water_temp} deg C")

File ~\C-SHELPh-2.5.0\cshelph\cshelph.py:270, in get_water_temp(data_path, latitude, longitude) 266 sea_temp_xr = xr.open_zarr(fsspec.get_mapper('s3://mur-sst/zarr', anon=True),consolidated=True) 268 sea_temp = sea_temp_xr['analysed_sst'].sel(time=slice(start_date,end_date)) --> 270 sst = round(sea_temp.sel(lat=lat_med,lon=lon_med,method='nearest').load().values[0] - 273,2) 272 return sst

IndexError: index 0 is out of bounds for axis 0 with size 0

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Friday, June 23, 2023 7:29 AM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

Excellent, thanks for working all of this out. This isn't developed or tested on windows, so there's no guarantee that it can work. One way to check your environment credentials is:

conda list

As for the buffer argument, I updated the code recently so first uninstall cshelph.

pip uninstall cshelph

Then install it again:

pip install cshelph

If the error happens again, let me know and I'll update the code

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1604149970, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIFW5DWNZXLEI5WWDDTXMV4ZPANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

Ok, nearly there. Looks like it's having trouble getting the sea temp automatically. You can use the default value or have a quick look at the average sea temp for your area and pass it in using the water temp argument. In honesty the sea temp does impact the output much

slyoung20 commented 1 year ago

Currently I see 3 codes for seatemp, I'm using the c-shelph 2.5 version right now. But if I redownload it from Github it has a different code. What I have now:

def get_water_temp_redacted(data_path, latitude, longitude): ''' pull down surface water temperature along the track from the JpL GHRSST opendap website.

The GHRSST data are gridded tiles with dimension 17998 x 35999.
To get the specific grid tile of the SST, you must convert from lat, lon coordinates
to the gridded tile ratio of the SST data product using the coordinates of the IS2 data.
'''
# Get date from data filename
file_date = data_path[-33:-25]
year = file_date[0:4]
month = file_date[4:6]
day = file_date[6:8]
julian_day = str(datetime.strptime(file_date, '%Y%m%d').timetuple().tm_yday)
# Add zero in front of day of year string
zero_julian_date = julian_day.zfill(3)

# Calculate ratio of latitude from mid-point of IS2 track
lat_avg = latitude.mean()
lat_min = -90
lat_max = 90
scaled_lat_min = 0
scaled_lat_max = 17998

new_lat_ratio = round(((lat_avg - lat_min) / (lat_max - lat_min)) *
                (scaled_lat_max - scaled_lat_min) + scaled_lat_min)

# Calculate ratio of longitude from mid-point of IS2 track
lon_avg = longitude.mean()
lon_min = -180
lon_max = 180
scaled_lon_min = 0
scaled_lon_max = 35999

new_lon_ratio = round(((lon_avg - lon_min) / (lon_max - lon_min)) *
                (scaled_lon_max - scaled_lon_min) + lon_min)

# Access the SST data using the JpL OpenDap interface
url = 'https://opendap.jpl.nasa.gov/opendap/OceanTemperature/ghrsst/data/GDS2/L4/GLOB/JpL/MUR/v4.1/'\
    + str(year) + '/' + str(julian_day) + '/' + str(file_date) \
    + '090000-JpL-L4_GHRSST-SSTfnd-MUR-GLOB-v02.0-fv04.1.nc'

dataset = netCDF4.Dataset(url)

# Access the data and convert the temperature from K to C
sea_temp = dataset['analysed_sst'][0,new_lat_ratio, new_lon_ratio] - 273.15
return sea_temp

def get_water_temp(datapath, latitude, longitude): ''' pull down surface water temperature along the track from the MUR SST: https://aws.amazon.com/marketplace/pp/prodview-kvgy4vkuhavsc?sr=0-3&ref=beagle&applicationId=AWSMpContessa#overview. '''

Get date from data filename

file_date = data_path[-33:-25]

start_date = str(datetime.strptime(file_date + ' 00:00:00', '%Y%m%d %H:%M:%S'))
end_date = str(datetime.strptime(file_date + ' 23:59:59', '%Y%m%d %H:%M:%S'))

# Calculate ratio of latitude from mid-point of IS2 track
lat_med = np.median(latitude)

# Calculate ratio of longitude from mid-point of IS2 track
lon_med = np.median(longitude)

sea_temp_xr = xr.open_zarr(fsspec.get_mapper('s3://mur-sst/zarr', anon=True),consolidated=True)

sea_temp = sea_temp_xr['analysed_sst'].sel(time=slice(start_date,end_date))

sst = round(sea_temp.sel(lat=lat_med,lon=lon_med,method='nearest').load().values[0] - 273,2)

return sst

If I download from github now it has:

def get_water_temp(data_path, latitude, longitude):

try:
    auth = earthaccess.login(strategy="netrc")
except:
    print("Login credentials not found. Sign in manually, your netrc file will be created for next time")
    auth = earthaccess.login(strategy="interactive", persist=True)

# Get date from data filename
file_date = data_path[-33:-25]

date_range = file_date[0:4] + '-' + file_date[4:6] + '-' + file_date[6:]

location_df = pd.DataFrame({'longitude':longitude,'latitude':latitude})

location_df = location_df.dropna(axis=0)

minx, miny, maxx, maxy = np.min(location_df['longitude']), np.min(location_df['latitude']), np.max(location_df['longitude']), np.max(location_df['latitude'])

lat_med = np.median(location_df['latitude'])
lon_med = np.median(location_df['longitude'])

Query = earthaccess.collection_query()

# Use chain methods to customize our query
collections = Query.keyword('GHRSST Level 4 CMC0.1deg Global Foundation Sea Surface Temperature Analysis').bounding_box(minx,miny,maxx,maxy).temporal(date_range,date_range).get(10)

short_name = collections[0]["umm"]["ShortName"]

Query = earthaccess.granule_query().short_name(short_name).version("3.0").bounding_box(minx,miny,maxx,maxy).temporal("2020-01-01","2020-01-01")

granules = Query.get(10)

ds_L3 = xr.open_mfdataset(earthaccess.open(granules),combine='nested',concat_dim='time',coords='minimal')

sea_temp = ds_L3['analysed_sst'].sel(lat=lat_med,lon=lon_med,method='nearest').load()

sst = round(np.nanmedian(sea_temp.values)-273,2)

return sst

Which version is better to use?

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Friday, June 23, 2023 1:17 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

Ok, nearly there. Looks like it's having trouble getting the sea temp automatically. You can use the default value or have a quick look at the average sea temp for your area and pass it in using the water temp argument. In honesty the sea temp does impact the output much

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1604580055, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQID7OKFD4Z7RCEBEN7LXMXFRTANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

That code should be in both. The first one is called redacted, which means it is no longer in use. It is not used in the code only the second one is used :)

slyoung20 commented 1 year ago

Yes, I know that. The other one is this one: def get_water_temp(data_path, latitude, longitude):

try:
    auth = earthaccess.login(strategy="netrc")
except:
    print("Login credentials not found. Sign in manually, your netrc file will be created for next time")
    auth = earthaccess.login(strategy="interactive", persist=True)

# Get date from data filename
file_date = data_path[-33:-25]

date_range = file_date[0:4] + '-' + file_date[4:6] + '-' + file_date[6:]

location_df = pd.DataFrame({'longitude':longitude,'latitude':latitude})

location_df = location_df.dropna(axis=0)

minx, miny, maxx, maxy = np.min(location_df['longitude']), np.min(location_df['latitude']), np.max(location_df['longitude']), np.max(location_df['latitude'])

lat_med = np.median(location_df['latitude'])
lon_med = np.median(location_df['longitude'])

Query = earthaccess.collection_query()

# Use chain methods to customize our query
collections = Query.keyword('GHRSST Level 4 CMC0.1deg Global Foundation Sea Surface Temperature Analysis').bounding_box(minx,miny,maxx,maxy).temporal(date_range,date_range).get(10)

short_name = collections[0]["umm"]["ShortName"]

Query = earthaccess.granule_query().short_name(short_name).version("3.0").bounding_box(minx,miny,maxx,maxy).temporal("2020-01-01","2020-01-01")

granules = Query.get(10)

ds_L3 = xr.open_mfdataset(earthaccess.open(granules),combine='nested',concat_dim='time',coords='minimal')

sea_temp = ds_L3['analysed_sst'].sel(lat=lat_med,lon=lon_med,method='nearest').load()

sst = round(np.nanmedian(sea_temp.values)-273,2)

return sst

Either one I try though still returns the same error.

Any ideas?

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Friday, June 23, 2023 1:35 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

That code should be in both. The first one is called redacted, which means it is no longer in use. It is not used in the code only the second one is used :)

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1604607492, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIF4WILRUM5HJEECQTDXMXHVZANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

slyoung20 commented 1 year ago

I noticed your original file path stated that the data was "processed". Did you select the layer you needed from the h5 file before running C-Shelph? Or what other processing did you have to do? I had a hard time selecting the layer I needed in ArcGIS from the h5 file.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Friday, June 23, 2023 1:35 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

That code should be in both. The first one is called redacted, which means it is no longer in use. It is not used in the code only the second one is used :)

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1604607492, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIF4WILRUM5HJEECQTDXMXHVZANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

It says processed just because I only downloaded the data that I needed. The datafile you have is fine.

If you pass in the -wt argument along with an integer value, it should run. Have you tried this?

slyoung20 commented 1 year ago

The problem is I need it to run for several areas with hundreds of files, so it would be best if it could automatically grab the SST. Let me try it just to see if I have other issues. I'm kind of concerned because it says the : index 0 is out of bounds for axis 0 with size 0, that makes me think that it isn't pulling any geographic information.

It's running again after I tried updating some of the packages. After that I'll try it with the SST passed in just to see what I get and let you know.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Friday, June 23, 2023 3:21 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

It says processed just because I only downloaded the data that I needed. The datafile you have is fine.

If you pass in the -wt argument along with an integer value, it should run. Have you tried this?

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1604765209, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIHZH4BPF5HTXOZS5ETXMXUC5ANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

Yes, it's not funding any geographic data. I'm back in the office Tuesday so can look in detail then if you give me a filename. You can still run this hundreds of times and pass in -wt each time using a loop

slyoung20 commented 1 year ago

Well, for different dates there will be different average temps. This is working so far, still running. I think I can work with it that way, minor inconvenience. I'll let you know what I get when it finishes.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Friday, June 23, 2023 3:33 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

Yes, it's not funding any geographic data. I'm back in the office Tuesday so can look in detail then if you give me a filename. You can still run this hundreds of times and pass in -wt each time using a loop

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1604781139, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIHPRHOGCHYVS37HSHTXMXVP3ANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

slyoung20 commented 1 year ago

OK it ran, and completed. No more errors. This is the output from the second to last section. Is this what it should look like? [cid:03e11e47-aff8-4336-91e5-41e36dc1c37d] Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Friday, June 23, 2023 3:33 PM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

Yes, it's not funding any geographic data. I'm back in the office Tuesday so can look in detail then if you give me a filename. You can still run this hundreds of times and pass in -wt each time using a loop

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1604781139, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIHPRHOGCHYVS37HSHTXMXVP3ANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

Sherry, were you able to get cshelph working satisfactorily? The trickiest part now that you have the software running is tuning the parameters. Cshelph will not work well under all conditions. It is designed to perform best in clear shallow waters so is very study site dependent. The example in my notebook shows an ideal scenario. If there are no other questions related to this issue I will close it out. you can always ask any new questions under a new ticket

slyoung20 commented 1 year ago

Hi Nathan,

Thank you. Yes, I did. Sorry for not getting back to you sooner. For now I'm manually entering the SST. I was wondering if you corrected the output to MLLW and if you did, what you used? I know for the US and US owned territories you can use VDatum, but outside the US I'm having a hard time finding a premade tool for conversion.

I have an idea I want to try for handling murky water. We'll see how that works.

Thank you so much for your assistance,

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Monday, June 26, 2023 9:22 AM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

Sherry, were you able to get cshelph working satisfactorily? The trickiest part now that you have the software running is tuning the parameters. Cshelph will not work well under all conditions. It is designed to perform best in clear shallow waters so is very study site dependent. The example in my notebook shows an ideal scenario. If there are no other questions related to this issue I will close it out. you can always ask any new questions under a new ticket

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1607466253, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIHTNXZVJRIIQBPPY7TXNGEHVANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

ok cool. ket me now how it goes. I do no MLLW correction. I transform the photons from ellipsoid (WGS84) to geoid (EGM2008) height, but that's it. Further corrections could be made by the user. Can you give me a filename you are using, I want to check out why the sea surface temp retrieval isn't working. Might take me a few days to get on to it though

slyoung20 commented 1 year ago

The file I tried first was ATL03_20230308145618_11921807_006_01.h5http://localhost:8888/edit/ATL03_20230308145618_11921807_006_01.h5

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Tuesday, June 27, 2023 10:03 AM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

ok cool. ket me now how it goes. I do no MLLW correction. I transform the photons from ellipsoid (WGS84) to geoid (EGM2008) height, but that's it. Further corrections could be made by the user. Can you give me a filename you are using, I want to check out why the sea surface temp retrieval isn't working. Might take me a few days to get on to it though

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1609576397, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIFNXTUMYWJKRWLUUUTXNLR4BANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

slyoung20 commented 1 year ago

Good afternoon Dr. Thomas,

I was wondering if you masked land before running the code? For example, most of the transects along Andros (Bahamas) go right over the island.

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Tuesday, June 27, 2023 10:03 AM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

ok cool. ket me now how it goes. I do no MLLW correction. I transform the photons from ellipsoid (WGS84) to geoid (EGM2008) height, but that's it. Further corrections could be made by the user. Can you give me a filename you are using, I want to check out why the sea surface temp retrieval isn't working. Might take me a few days to get on to it though

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#issuecomment-1609576397, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIFNXTUMYWJKRWLUUUTXNLR4BANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

slyoung20 commented 1 year ago

Good afternoon Dr. Thomas,

Thank you for all your previous assistance. I've managed to get the code fully working and I'm cleaning the data in Arc. The last issue I'm having, is I can't seem to get start_lat and end_lat to work. What else do I need to add and where should I add it?

Thank you,

Sherry Young

PhD student, graduate instructor Dept. of Geography and Geoinformation Sciences George Mason University 4400 University Dr. Fairfax, VA 22030

@.***

From: Nathan Thomas @.> Sent: Tuesday, June 27, 2023 10:03 AM To: nmt28/C-SHELPh @.> Cc: Sherry L Young @.>; Author @.> Subject: Re: [nmt28/C-SHELPh] Error creating Transformer from CRS (Issue #11)

Closed #11https://github.com/nmt28/C-SHELPh/issues/11 as completed.

— Reply to this email directly, view it on GitHubhttps://github.com/nmt28/C-SHELPh/issues/11#event-9652737868, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWCQIFNXTUMYWJKRWLUUUTXNLR4BANCNFSM6AAAAAAZMK66RQ. You are receiving this because you authored the thread.Message ID: @.***>

nmt28 commented 1 year ago

Hey Sherry, can you post this as a new issue? It's easier to keep track of. I may be able to take a look at this, this week