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DeDop is a User Configurable Tool for Processing Delay Doppler Altimeter Data.

Home Page: http://dedop.org/

License: GNU General Public License v3.0

Python 39.75% Jupyter Notebook 60.25%

altimeter backend backend-services cli delay-doppler processor python tornado

dedop-core's Introduction

DeDop³

DeDop is a User Configurable Tool for Processing Delay Doppler Altimeter Data. "DeDop" stands for Delay Doppler (Altimeter) Processor.

For more information about the project please visit www.dedop.org. For more information about the software have a look into the DeDop User Manual.

setup.py - main build script to be run with Python 3.5
dedop/ - main package and production code
test/ - test package and test code
docs/ - documentation in Sphinx/RST format
notebooks/ - some IPython notebooks demonstrating the use of the DeDop Python API

Installation using installer (recommended)

Instructions on how to get the installer and how to install are available here.

Installation from Sources

Using Conda

We recommend installing DeDop into an isolated Python 3 environment, because this approach avoids clashes with existing versions of DeDop's 3rd-party module requirements. We recommend using Conda (Miniconda or Anaconda) which will usually also avoid platform-specific issues caused by module native binaries.

Creating an isolated environment for DeDop. This will require around 2.2 GB disk space on Linux/Darwin and and 1.2 GB on Windows. To create a new DeDop environment dedop in your Anaconda/Miniconda installation directory, type:

$ conda env create --file environment.yml

If you want the environment to be installed in another location, e.g. due to disk space limitations, type:

$ conda env create --file environment.yml --prefix some/other/location/for/dedop

Next step is to activate the new environment. On Linux/Darwin type:

$ source activate dedop

In case you used another location use it instead of the name dedop. Windows users can omit the source command and just type

> activate dedop

You can now safely install and run DeDop sources into the new dedop environment.

(dedop) $ python setup.py develop

To permanently install DeDop into the Python environment (not recommended while in development mode!), type:

(dedop) $ python setup.py install

Using Standard Python

DeDop requires Python 3.5+.

DeDop can be run from sources directly, once the following module requirements are resolved:

numpy
scipy
netcdf4
numexpr
pyproj

If you like to perform L1B product analysis tasks with DeDop using an IPython Notebook, then also install:

jupyter
ipywidgets
matplotlib
bokeh

The most up-to-date and complete list of module requirements is found in the project's environment.yml file.

To install and run DeDop from sources directly, type:

$ python setup.py develop

To permanently install DeDop into Python (not recommended while in development mode!), type:

$ python setup.py install

Getting started

Command Line Interface

To test the installation from source, first run the DeDop command-line interface. Type

$ dedop -h

More examples are available here http://dedop-core.readthedocs.io/en/latest/manual.html#examples

Web API

This is required by dedop-studio. To start the web API, type:

$ dedop-webapi start

A random port number will be assigned unless explicitly specified on the command like so:

$ dedop-webapi --port 2999 start

To check if the wbe API has started successfully, open your browser and enter the web API URL. The following response should be displayed:

{"status": "ok", "content": {"name": "dedop-webapi", "version": "1.0.0", "timestamp": "2017-05-16"}}

To stop, go to [host_name]:[port_number]/exit on the browser. For example:

127.0.0.1:2999/exit

License

DeDop is distributed under the terms and conditions of the MIT license.

dedop-core's People

Contributors

Stargazers

Watchers

Forkers

alexaputnam dallasmasters dedop-cotton dalavancloud ouc-cook furniture17 xxzhao1997 whigg

dedop-core's Issues

Allow for easy installing from source code

Users currently face a problem installing dedop-core from source using python3 setup.py install.

Fix: make the cate-util dependency optional, it is used by dedop-webapi only, which in turn is only used by dedop-studio.

Error while running DeDop

Hi, I am a new user and just installed the dedop-core onto a linux. I received the following error while trying to run DeDop, and following the Quick Start instructions (http://dedop.readthedocs.io/en/latest/quickstart.html) using the test_data provided by dedop-core (/dedop-core/test_data/data/test_l1a/inputs/l1a_test.nc):

raise RuntimeWarning("MAX_ITERS reached in ecef2lla")

RuntimeWarning: MAX_ITERS reached in ecef2lla

Apart from this error, is this DeDop project ready for prime time?

Thank you.

DeDop Studio can't be opened because it is from an unidentified developer MacOSX

DeDop Studio cannot be opened because the installer is not signed with an Apple Developer certificate. This happens when default security configuration of "Allow apps downloaded from: App Store" is selected.

OS: MacOSX 10.13.3
DeDop Studio: 1.3.0

Apply AGC correction to input and output waveforms

We need to apply the AGC factor when reading L1A files. This is done as:

waveform = (i_meas_ku + 1j * q_meas_ku) / 10 ^ (-agc / 20)

When writing the L1B, the AGC is applied:

i2q2_meas_ku = wfm_multilooked * 10 ^ (-agc / 10)

and when writing the L1BS stack data, a the dynamic scale factor needs to be computed, applied, and written to the file.

related to the bug in issue #27

[documentation] Information on using CS2-L1A DBL files

I am a new user and am having trouble figuring out how to input the Cryosat-L1A .DBL files distributed by ESA. Could you provide some documentation on how to either convert these into the .nc format used by the command line utils or how to use .DBL files directly with the DEDOP command line util.

L1B Sigma0 values

Values of Sigma-0 at L1B do not match the values from ESA S3 IPF files (sentinel-3 data). Need to determine whether the values from dedop are correct, and if not, update the calculation of sigma-0

Surface Locations

Summary:

Implement the Surface Locations algorithm of the SAR L1B processing chain.

The Surface Locations algorithm computes the locations and corresponding datation and orbit parameters defined by the intersection of the Doppler beams and estimated surface positions along the satellite track.

Algorithm description:

Generate surface locations derived from the burst positions along the satellite's track. These positions are estimated using the window delay.
initialize output variables for the first surface location, based on the variables of the burst from which it was calculated.
Compute the angular azimuth beam resolution at the current satellite position, and determine where this direction intersects with the surface.
Interpolate values for a new surface location at the position of this intersection.
Perform an interpolation to estimate the configuration of the satellite's orbit associated with the new surface location.

Stack is not centred and not symmetric if radial velocity is high

need to update beam-angles algorithm to correctly centre the stack

`dedop output compare` fails on windows with long file names

Expected behavior

running dedop output compare (or launching the comparison from DeDop Studio) launches the comparison notebook.

Actual behavior

The notebook fails to launch. In DeDop Studio, an error message is shown.

Steps to reproduce the issue

Add a file with a long filename to the workspace
Process with two configurations
Attempt to compare the output files with each other

Specifications

DeDop 1.5.1, Windows 7.

Strange behaviour of STDEV_STACK_L1B_ECHO_SAR_KU

Comparing against CryoSat L1b data after processing the file L1B_CS_LTA__SIR1SAR_FR_20120329T112952_20120329T113436_C001.DBL through DeDop (after conversion to L1A), different behaviour of the stack standard deviation parameter is seen. In CS L1b, the parameter varies from 0–5000. In DeDop data, the parameter is clustered around 0, with a population at 0.5. Then there is a group of values around 4300, with nothing between.

Apply CoG correction to Range

Need to apply CoG correction to range (window delay) when reading L1A files

Output terminates early in Amazon basin data

L1B products have very poor coverage despite data being available in L1A (see plots below):

stack level sigma0

write stack-level (per beam) sigma0 values to the L1B-S output file

`--traceback` not enabled for the `run` command

running dedop -h lists an optional --traceback flag, which will display the full Python traceback if the processor encounters an error. However, this option isn't enabled on the dedop run command, which is where it would be most useful.

running dedop run --traceback generates the error:

usage: dedop [-h] [--version] [--traceback] [--license] [--docs] COMMAND ...
dedop: error: unrecognized arguments: --traceback

[documentation] Update the installation instruction to use a specific Python version to prevent incompatibility

The detail of the problem can be found in this issue.

Crash in multilooking algorithm

Failure to fit a Gaussian curve during multilooking can sometimes cause crashes or multiple error messages being printed to the terminal.

Make the CLI backward compatible

This is a feature request to fix this bug.

In the case of re-installation/upgrade, users shall still be able to do processing.

list index out of range error

Expected behavior

DeDop can process Amazon L1A file.

Actual behavior

Observed a list index out of range error.

In DeDop Shell, it looks like this.

> dedop run -i "C:\Users\hans\.dedop\workspaces\aaa\inputs\CS_LTA__SIR1SAR_FR_20130303T030418_20130303T030503_C001.DBL.nc"
processing C:\Users\hans\.dedop\workspaces\aaa\inputs\CS_LTA__SIR1SAR_FR_20130303T030418_20130303T030503_C001.DBL.nc using "default"
processing: done
dedop run: error: list index out of range

Steps to reproduce the issue

With DeDop Studio

Download this L1A input file
In DeDop Studio, run a process for those files with default configuration

With DeDop Core

Run in DeDop Shell dedop run -i "\path\to\CS_LTA__SIR1SAR_FR_20130303T030418_20130303T030503_C001.DBL.nc"

Specifications

DeDop-core: v1.1.0 (based on this commit 8c22492)
DeDop-studio: v1.1.0
OS: Windows 10

Provide template for new issues

Add an issue template for new issues regarding DeDop CLI and DeDop Studio.

Issue with Amazon data

Expected behavior

Able to process Amazon L1A files

Actual behavior

Steps to reproduce the issue

Download the following L1A input files:
- file1
- file2
- file3
In DeDop Studio, run a process for those files with default configuration

Specifications

dedop-0.5.4.dev
dedop-studio-0.0.1-dev

Corrections & Calibrations

A number of corrections need to be implemented in the dedop-core processor.

apply window delay corrections
apply intra-burst corrections:
- application of CAL1 intra-burst
- application of CAL2

Documentation fix: include numexpr library in the "installation from source" instruction

numexpr has now been used in DeDop processor, but not yet included in the documentation. As a result the following error occurred:

(dedop) jeant@kami:/home/kami/jeant/dedop$ dedop
Traceback (most recent call last):
  File "/home/kami/jeant/miniconda3/envs/dedop/bin/dedop", line 11, in <module>
    load_entry_point('dedop', 'console_scripts', 'dedop')()
  File "/home/kami/jeant/miniconda3/envs/dedop/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 565, in load_entry_point
  File "/home/kami/jeant/miniconda3/envs/dedop/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2598, in load_entry_point
  File "/home/kami/jeant/miniconda3/envs/dedop/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2258, in load
  File "/home/kami/jeant/miniconda3/envs/dedop/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2264, in resolve
  File "/home/kami/jeant/dedop/dedop/ui/cli.py", line 19, in <module>
    from dedop.proc.sar import L1BProcessor
  File "/home/kami/jeant/dedop/dedop/proc/sar/__init__.py", line 1, in <module>
    from .processor import L1BProcessor
  File "/home/kami/jeant/dedop/dedop/proc/sar/processor.py", line 13, in <module>
    from .algorithms import *
  File "/home/kami/jeant/dedop/dedop/proc/sar/algorithms/__init__.py", line 3, in <module>
    from .geometry_corrections import GeometryCorrectionsAlgorithm
  File "/home/kami/jeant/dedop/dedop/proc/sar/algorithms/geometry_corrections.py", line 2, in <module>
    import numexpr as ne
ImportError: No module named 'numexpr'

No module named 'jupyter_core'

Running ' dedop output inspect <output_file>' resulted the following error:

 Traceback (most recent call last):
  File "C:\Users\hans\DeDop-core\Scripts\jupyter-notebook-script.py", line 3, in <module>
    import notebook.notebookapp
  File "C:\Users\hans\DeDop-core\lib\site-packages\notebook\__init__.py", line 25, in <module>
    from .nbextensions import install_nbextension
  File "C:\Users\hans\DeDop-core\lib\site-packages\notebook\nbextensions.py", line 23, in <module>
    from jupyter_core.paths import (
ModuleNotFoundError: No module named 'jupyter_core'

This is very similar to CCI-Tools/cate#397.

User unable to process because the configurations have changed in the new installer

This is a follow-up ticket from an issue reported by @cmray #8

Scenario

Install DeDop Shell v0.5.1
Do a processing
- dedop i add <L1A input file>
- dedop run
Install DeDop Shell v0.5.2
Do a processing
- dedop run

Problem

A string of errors are thrown by DeDop Shell that say unknown parameters. Look at this (issue)[https://github.com//issues/8] for more details on the error.

This problem occurred because there are parameter changes in the default configuration files of v0.5.2 and the processor does not support the old parameters anymore (from v0.5.1 or before). When a user installs a new version (with or without uninstalling the old one), the ~/.dedop directory stays unless when it is intentionally removed.

Installation from source: Conflict between matplotlib and python 3.6.0-0

Hi All,

I was trying to install DeDop from source following the "Installation from source" instructions. The process hung with the command
conda install matplotlib bokeh jupyter ipywidgets

I have included the log of the complete installation process below.

-Chris

CRAY:~ cray$ conda create -n dedop python=3
Fetching package metadata .......
Solving package specifications: ..........

Package plan for installation in environment /Users/cray/miniconda2/envs/dedop:

The following NEW packages will be INSTALLED:

openssl:    1.0.2j-0     
pip:        9.0.1-py36_1 
python:     3.6.0-0      
readline:   6.2-2        
setuptools: 27.2.0-py36_0
sqlite:     3.13.0-0     
tk:         8.5.18-0     
wheel:      0.29.0-py36_0
xz:         5.2.2-1      
zlib:       1.2.8-3

Proceed ([y]/n)? y

Linking packages ...
[ COMPLETE ]|#############################################################| 100%

To activate this environment, use:

> source activate dedop

To deactivate this environment, use:

> source deactivate dedop

CRAY:~ cray$ source activate dedop
(dedop) CRAY:~ cray$ conda install numpy scipy netcdf4
Fetching package metadata .......
Solving package specifications: ..........

Package plan for installation in environment /Users/cray/miniconda2/envs/dedop:

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
jpeg-8d                    |                2         145 KB
curl-7.49.0                |                1         493 KB
hdf4-4.2.12                |                0         642 KB
hdf5-1.8.17                |                1         1.7 MB
libnetcdf-4.4.1            |                0         868 KB
numpy-1.11.2               |           py36_0         3.3 MB
netcdf4-1.2.4              |      np111py36_1         550 KB
scipy-0.18.1               |      np111py36_0        13.5 MB
------------------------------------------------------------
                                       Total:        21.1 MB

The following NEW packages will be INSTALLED:

curl:      7.49.0-1          
hdf4:      4.2.12-0          
hdf5:      1.8.17-1          
jpeg:      8d-2              
libnetcdf: 4.4.1-0           
mkl:       11.3.3-0          
netcdf4:   1.2.4-np111py36_1 
numpy:     1.11.2-py36_0     
scipy:     0.18.1-np111py36_0

Proceed ([y]/n)? y

Fetching packages ...
jpeg-8d-2.tar. 100% |##########################################| Time: 0:00:00 2.07 MB/s
curl-7.49.0-1. 100% |##########################################| Time: 0:00:00 2.56 MB/s
hdf4-4.2.12-0. 100% |##########################################| Time: 0:00:00 2.66 MB/s
hdf5-1.8.17-1. 100% |##########################################| Time: 0:00:00 2.74 MB/s
libnetcdf-4.4. 100% |##########################################| Time: 0:00:00 2.56 MB/s
numpy-1.11.2-p 100% |##########################################| Time: 0:00:01 2.40 MB/s
netcdf4-1.2.4- 100% |##########################################| Time: 0:00:00 1.14 MB/s
scipy-0.18.1-n 100% |##########################################| Time: 0:00:05 2.75 MB/s
Extracting packages ...
[ COMPLETE ]|#############################################################| 100%
Linking packages ...
[ COMPLETE ]|#############################################################| 100%
(dedop) CRAY:~ cray$ conda install matplotlib bokeh jupyter ipywidgets
Fetching package metadata .......
Solving package specifications: ....

UnsatisfiableError: The following specifications were found to be in conflict:

matplotlib
python 3.6*
Use "conda info " to see the dependencies for each package.

(dedop) CRAY:~ cray$

Error when listing configurations of empty workspace

Scenario

dedop w add newWorkSpace
dedop c ls

Issue

> dedop c ls
Traceback (most recent call last):
  File "C:\Users\hans\DeDop\Scripts\dedop-script.py", line 5, in <module>
    sys.exit(dedop.ui.cli.main())
  File "C:\Users\hans\DeDop\lib\site-packages\dedop\ui\cli.py", line 1268, in main
    status_and_message = args_obj.command_class().execute(args_obj)
  File "C:\Users\hans\DeDop\lib\site-packages\dedop\ui\cli.py", line 512, in execute
    return command_args.cf_command(command_args)
  File "C:\Users\hans\DeDop\lib\site-packages\dedop\ui\cli.py", line 646, in execute_list
    num_configs = len(config_names)
TypeError: object of type 'NoneType' has no len()

DeDop Core installation failed in Linux and MacOS: post-link failed for: widgetsnbextension

Expected behavior

DeDop Core installs successfully

Actual behavior

It fails when installing the dependency packages, specifically when installing widgestsnbextension. The error message shown is: Error: post-link failed for: widgetsnbextension-2.0.1-py36_0. Possibly related to conda-forge/widgetsnbextension-feedstock#18

Steps to reproduce the issue

Download installer file DeDop-core-1.5.0-Linux-x86_64.sh or DeDop-core-1.5.0-MacOSX-x86_64.sh
Run the installer
Observe an error during the installation

Specifications

dedop version: DeDop-core 1.5.0
OS: Ubuntu 18.04.1 LTS

Azimuth processing method selection flags

The flags for selecting azimuth processing method are inconsistent with e.g. azimuth windowing method, and need to be updated

Possible typo in documentation for conda activation

Docs/Installation/From Source says

conda create -n dedop python=3
source activate.sh dedop

command actually needed (using Anaconda on OSX) was

source activate dedop

might be because I used Anaconda rather than Miniconda?

Add metadata to output files

consider adding metadata to output files (L1B & L1B-S)- netcdf parameters to indicate the processor used, configuration options etc.

numexpr missing in library dependencies of installer

I got the following errors

(dedop) .... /dedop$ dedop
Traceback (most recent call last):
...
    import numexpr as ne
ImportError: No module named 'numexpr'

incorrect L1BS start and stop stack look angles

the metadata and values for start_look_angle_stack_l1bs_echo_sar_ku and stop_look_angle_stack_l1bs_echo_sar_ku are not correct.

The long_name metadata fields of these variables are given as "doppler beam angles in stack: l1bs_echo_sar_ku mode" and "stop doppler beam angle in stack: l1bs_echo_sar_ku mode".

The values written to the variable are all 2^15-1 (maximum short value)

Corrections to L1B variables

Some L1B variables are being computed wrongly/omitted. These include:

surf_type_l1b_echo_sar_ku
uso_cor_l1b_echo_sar_ku
agc_cor_l1b_echo_sar_ku
max_stack_l1b_echo_sar_ku

Surface Focusing

Add surface focusing options to the Surface Locations algorithm. This will allow the user to specify a target location (in geodetic coordinates) to which the processor shall create a focused output record.

update surface locations algorithm (single target)
add/update CNF parameters (single target)
unit tests (single target)
update surface locations algorithm (sequence of surfaces)
add/update CNF parameters (sequence of surfaces)
unit tests (sequence of surfaces)

`dedop config upgrade` fails to upgrade v1.4.0 configurations to v1.5.0

Expected behavior

After installing v1.5.0, the command dedop config upgrade will upgrade existing configurations to the latest version.

Actual behavior

The command fails

Steps to reproduce the issue

Install a version of dedop < v1.5.0
create a configuration
Install v1.5.0
Attempt to run dedop config upgrade

Specifications

all platforms

Enable selection of reconditioned-cryosat CHD when creating a new configuration profile

Currently the default CHD parameter values for dedop are suitable only for use with Sentinel-3 data. While this should remain the default behaviour, users should have the option to create a configuration profile with a CHD suitable for processing reconditioned cryosat FBR data.

add reconditioned cryosat CHD to the repository
enable workspace manager to create configurations from this template
add option to dedop config add command to use the cryosat template

Try hard linking netCDF files to workspace folder instead of copying

Expected behavior

dedop should try to make hard links of input netCDF files instead of copying them to the workspace when:

on a Unix-like system,
workspace and source L1A files are on the same data volume (otherwise hard linking is impossible to do).

Alternatively, dedop could set up symbolic links on Unix-like systems or shortcuts (if judged reliable) on Windows systems. For Windows shortcuts & Unix-like symlinks, this should be triggered by a new dedop option to the =dedop input add files= command (e.g. "--links" option).

Actual behavior

dedop always copies files resulting in disk space waste.

Steps to reproduce the issue

Make a workspace and add inputs files to it.

Specifications

This request concerns only Linux & Unix-like users and maybe MACOSX users.

Run dedop-core with Python 3.6

Test dedop-core to run with Python 3.6. This is to enable using newer version of cate-util, which is about to migrate to Python 3.6.

Test CLI
Test webapi
Test Processors
Test Backend Installer

`Math Domain Error` in processing some S3 data

This is being caused by incorrect application of the waveform scale factor when reading L1A files

conda environment cannot be created: The following specifications were found to be incompatible with your CUDA driver

Expected behavior

conda env create --file environment.yml

should run without any errors and create the conda environment as defined in environment.yml.

Actual behavior

When creating the conda environment, conda tries to solve found conflicts and fails to do so. It might have something to do with my CUDA driver.
How could I deal with this incompatibility?

Steps to reproduce the issue

git clone {dedop-core-git-repo}
cd dedop-core
conda env create --file environment.yml

Specifications

OS: Ubuntu 18.04 LTS
conda version 4.8.3

Console output

~/repos/dedop-core$ conda env create --file environment.yml
Collecting package metadata (repodata.json): done
Solving environment: \ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                            |                                                                                                                                     
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                            /                                                                                                                                     

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package numpy conflicts for:
scipy==1.0.0 -> numpy[version='>=1.9|>=1.9.3,<2.0a0']
bokeh==0.12.13 -> numpy[version='>=1.7.1']
matplotlib==2.0.2 -> numpy
numexpr==2.6.4 -> numpy[version='>=1.11|>=1.8|>=1.9.3,<2.0a0']
netcdf4==1.2.4 -> numpy[version='1.10.*|1.11.*|1.12.*']
numpy==1.11.3
pyproj==1.9.5.1 -> numpy

Package libffi conflicts for:
pytest-cov -> python -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
numpy==1.11.3 -> python[version='>=3.6,<3.7.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
cate-util==1.1.0.dev1=py36_0 -> python[version='>=3.6,<3.7.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
matplotlib==2.0.2 -> python[version='>=3.6,<3.7.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
tornado[version='>=4.0,<5.0'] -> python[version='>=3.8,<3.9.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
netcdf4==1.2.4 -> python=3.6 -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
numexpr==2.6.4 -> python=3.6 -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
ipywidgets==7.1.1 -> python=3.6 -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
bokeh==0.12.13 -> python=3.6 -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
jupyter==1.0.0 -> python -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
pytest -> python[version='>=3.8,<3.9.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
pyproj==1.9.5.1 -> python[version='>=3.6,<3.7.0a0'] -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']
scipy==1.0.0 -> python=3.6 -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.3,<3.4.0a0|>=3.2.1,<3.3a0']

Package setuptools conflicts for:
bokeh==0.12.13 -> jinja2[version='>=2.7'] -> setuptools
netcdf4==1.2.4 -> setuptools
matplotlib==2.0.2 -> setuptools
pytest-cov -> setuptools
pytest -> setuptools[version='>=40.0']
pytest-cov -> pytest[version='>=4.6'] -> setuptools[version='>=40.0']
ipywidgets==7.1.1 -> ipython[version='>=4.0.0'] -> setuptools[version='>=18.5']
python==3.6 -> pip -> setuptools
numexpr==2.6.4 -> setuptools

Package six conflicts for:
bokeh==0.12.13 -> python-dateutil[version='>=2.1'] -> six[version='>=1.5']
pytest -> six[version='>=1.10.0']
numpy==1.11.3 -> mkl-service[version='>=2,<3.0a0'] -> six
tornado[version='>=4.0,<5.0'] -> singledispatch -> six
pytest-cov -> pytest[version='>=4.6'] -> six[version='>=1.10.0']
pytest -> more-itertools[version='>=4.0'] -> six[version='>=1.0.0,<2.0.0']
matplotlib==2.0.2 -> cycler[version='>=0.10'] -> six[version='>=1.5']
ipywidgets==7.1.1 -> traitlets[version='>=4.3.1,<5.0.0'] -> six
bokeh==0.12.13 -> six[version='>=1.5.2']

Package certifi conflicts for:
matplotlib==2.0.2 -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
bokeh==0.12.13 -> tornado[version='>=4.3'] -> certifi
numexpr==2.6.4 -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
pytest-cov -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
pytest -> setuptools[version='>=40.0'] -> certifi[version='>=2016.09|>=2016.9.26']
netcdf4==1.2.4 -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
tornado[version='>=4.0,<5.0'] -> certifi

Package python conflicts for:
pytest -> more-itertools[version='>=4.0'] -> python[version='3.7.*|3.8.*|>=3.4|>=3.8.0a,<3.9.0a0']
bokeh==0.12.13 -> jinja2[version='>=2.7'] -> python[version='3.4.*|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0']
python==3.6
pytest -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0|3.4.*']
cate-util==1.1.0.dev1=py36_0 -> python[version='>=3.6,<3.7.0a0']
netcdf4==1.2.4 -> python[version='2.7.*|3.5.*|3.6.*|3.4.*']
pytest-cov -> coverage[version='>=4.4'] -> python[version='>=3.8,<3.9.0a0']
scipy==1.0.0 -> python[version='2.7.*|3.5.*|3.6.*|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=2.7,<2.8.0a0']
matplotlib==2.0.2 -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']
ipywidgets==7.1.1 -> python[version='2.7.*|3.5.*|3.6.*|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=2.7,<2.8.0a0']
tornado[version='>=4.0,<5.0'] -> backports_abc[version='>=0.4'] -> python
jupyter==1.0.0 -> python[version='2.7.*|3.5.*|3.6.*|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0']
bokeh==0.12.13 -> python[version='2.7.*|3.5.*|3.6.*|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=2.7,<2.8.0a0']
pyproj==1.9.5.1 -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
numexpr==2.6.4 -> python[version='2.7.*|3.5.*|3.6.*|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=2.7,<2.8.0a0']
pyproj==1.9.5.1 -> numpy -> python[version='2.7.*|3.5.*|3.6.*|>=3.8,<3.9.0a0|3.4.*']
numexpr==2.6.4 -> numpy[version='>=1.11'] -> python[version='3.4.*|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0']
matplotlib==2.0.2 -> cycler[version='>=0.10'] -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|<3']
ipywidgets==7.1.1 -> ipykernel[version='>=4.5.1'] -> python[version='3.4.*|>=3|>=3.4|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.5']
jupyter==1.0.0 -> ipykernel -> python[version='3.4.*|>=3|>=3.4|>=3.5']
scipy==1.0.0 -> numpy[version='>=1.9'] -> python[version='3.4.*|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0']
netcdf4==1.2.4 -> numpy=1.12 -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0']
pytest-cov -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
tornado[version='>=4.0,<5.0'] -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|3.4.*|>=3.5,<3.6.0a0']

Package zlib conflicts for:
matplotlib==2.0.2 -> freetype[version='>=2.8,<2.9.0a0'] -> zlib[version='1.2.*|1.2.11|1.2.8|1.2.11.*']
pytest-cov -> python -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
ipywidgets==7.1.1 -> python=3.6 -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
scipy==1.0.0 -> python=3.6 -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
matplotlib==2.0.2 -> zlib[version='>=1.2.11,<1.3.0a0']
cate-util==1.1.0.dev1=py36_0 -> python[version='>=3.6,<3.7.0a0'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8']
netcdf4==1.2.4 -> hdf5[version='1.8.17|1.8.17.*'] -> zlib[version='1.2.*|>=1.2.11,<1.3.0a0|1.2.11|1.2.8|1.2.11.*']
python==3.6 -> zlib=1.2
tornado[version='>=4.0,<5.0'] -> python[version='>=3.8,<3.9.0a0'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
hdf4==4.2.12 -> zlib=1.2
numpy==1.11.3 -> python[version='>=3.6,<3.7.0a0'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
bokeh==0.12.13 -> python=3.6 -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
jupyter==1.0.0 -> python -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
pyproj==1.9.5.1 -> python[version='>=3.6,<3.7.0a0'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
numexpr==2.6.4 -> python=3.6 -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']
pytest -> python[version='>=3.8,<3.9.0a0'] -> zlib[version='1.2.*|1.2.11|>=1.2.11,<1.3.0a0|1.2.8|1.2.11.*']

Package mkl_random conflicts for:
bokeh==0.12.13 -> numpy[version='>=1.7.1'] -> mkl_random[version='>=1.0.2,<2.0a0|>=1.0.4,<2.0a0']
pyproj==1.9.5.1 -> numpy -> mkl_random[version='>=1.0.2,<2.0a0|>=1.0.4,<2.0a0']
matplotlib==2.0.2 -> numpy -> mkl_random[version='>=1.0.2,<2.0a0|>=1.0.4,<2.0a0']
scipy==1.0.0 -> numpy[version='>=1.9'] -> mkl_random[version='>=1.0.2,<2.0a0|>=1.0.4,<2.0a0']
numexpr==2.6.4 -> numpy[version='>=1.11'] -> mkl_random[version='>=1.0.2,<2.0a0|>=1.0.4,<2.0a0']

Package python-dateutil conflicts for:
matplotlib==2.0.2 -> python-dateutil
bokeh==0.12.13 -> python-dateutil[version='>=2.1']

Package ca-certificates conflicts for:
netcdf4==1.2.4 -> python=2.7 -> ca-certificates
scipy==1.0.0 -> python=2.7 -> ca-certificates
jupyter==1.0.0 -> python -> ca-certificates
bokeh==0.12.13 -> python=2.7 -> ca-certificates
pytest-cov -> python -> ca-certificates
numexpr==2.6.4 -> python=2.7 -> ca-certificates
tornado[version='>=4.0,<5.0'] -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
pyproj==1.9.5.1 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
ipywidgets==7.1.1 -> python=2.7 -> ca-certificates
matplotlib==2.0.2 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
python==3.6 -> openssl=1.0 -> ca-certificates
numpy==1.11.3 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
pytest -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates

Package openblas-devel conflicts for:
numpy==1.11.3 -> openblas[version='>=0.3.3,<0.3.4.0a0'] -> openblas-devel[version='0.3.3|>=0.2.20,<0.2.21.0a0|0.3.6|0.3.6|0.3.6|>=0.3.2,<0.3.3.0a0',build='2|1|2|3|1|0']
scipy==1.0.0 -> openblas[version='0.2.20|0.2.20.*'] -> openblas-devel[version='>=0.2.20,<0.2.21.0a0']

Package pyqt conflicts for:
matplotlib==2.0.2 -> pyqt=5.6
jupyter==1.0.0 -> qtconsole -> pyqt[version='4.11.*|5.6.*|>=5.6.0,<5.7.0a0|>=5.9.2,<5.10.0a0']

Package ssl_match_hostname conflicts for:
matplotlib==2.0.2 -> tornado -> ssl_match_hostname
bokeh==0.12.13 -> tornado[version='>=4.3'] -> ssl_match_hostname
tornado[version='>=4.0,<5.0'] -> ssl_match_hostname

Package tornado conflicts for:
jupyter==1.0.0 -> ipykernel -> tornado[version='>=4|>=4,<6|>=4.0|>=4.2|>=5.0|>=5.0,<7|>=4.1,<7']
tornado[version='>=4.0,<5.0']
bokeh==0.12.13 -> tornado[version='>=4.3']
matplotlib==2.0.2 -> tornado
ipywidgets==7.1.1 -> ipykernel[version='>=4.5.1'] -> tornado[version='>=4.0|>=4.2']

Package libgcc-ng conflicts for:
numpy==1.11.3 -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.2.0']
numpy==1.11.3 -> python[version='>=3.7,<3.8.0a0'] -> libgcc-ng[version='>=7.5.0|>=8.2.0']

Package pyparsing conflicts for:
matplotlib==2.0.2 -> pyparsing
pytest -> packaging -> pyparsing[version='>=2.0.2']

Package pytest conflicts for:
pytest
pytest-cov -> pytest[version='>=3.6|>=4.6']

Package _openmp_mutex conflicts for:
tornado[version='>=4.0,<5.0'] -> libgcc-ng[version='>=7.3.0'] -> _openmp_mutex[version='>=4.5']
matplotlib==2.0.2 -> libgcc-ng[version='>=7.2.0'] -> _openmp_mutex[version='>=4.5']
scipy==1.0.0 -> libgcc-ng[version='>=7.2.0'] -> _openmp_mutex[version='*|>=4.5',build=*_llvm]
numexpr==2.6.4 -> libgcc-ng[version='>=7.2.0'] -> _openmp_mutex[version='*|>=4.5',build=*_llvm]
pyproj==1.9.5.1 -> libgcc-ng[version='>=7.3.0'] -> _openmp_mutex[version='>=4.5']
numpy==1.11.3 -> libgcc-ng[version='>=7.3.0'] -> _openmp_mutex[version='*|>=4.5',build=*_llvm]

Package jinja2 conflicts for:
bokeh==0.12.13 -> jinja2[version='>=2.7']
jupyter==1.0.0 -> nbconvert -> jinja2

Package libstdcxx-ng conflicts for:
numpy==1.11.3 -> python[version='>=3.6,<3.7.0a0'] -> libstdcxx-ng[version='>=7.2.0|>=7.5.0']
numpy==1.11.3 -> libstdcxx-ng[version='>=4.9|>=7.3.0']

Package ipywidgets conflicts for:
jupyter==1.0.0 -> ipywidgets
ipywidgets==7.1.1

Package liblapacke conflicts for:
numpy==1.11.3 -> blas=[build=openblas] -> liblapacke==3.8.0[build='4_mkl|9_mkl|10_mkl|13_mkl|14_mkl|15_mkl|4_openblas|5_openblas|11_openblas|16_openblas|15_openblas|14_openblas|13_openblas|12_openblas|10_openblas|9_openblas|8_openblas|7_openblas|6_openblas|12_mkl|11_mkl|8_mkl|7_mkl|6_mkl|5_mkl']
scipy==1.0.0 -> blas=[build=openblas] -> liblapacke==3.8.0[build='4_mkl|9_mkl|10_mkl|13_mkl|14_mkl|15_mkl|4_openblas|5_openblas|11_openblas|16_openblas|15_openblas|14_openblas|13_openblas|12_openblas|10_openblas|9_openblas|8_openblas|7_openblas|6_openblas|12_mkl|11_mkl|8_mkl|7_mkl|6_mkl|5_mkl']
numexpr==2.6.4 -> blas=[build=openblas] -> liblapacke==3.8.0[build='4_mkl|9_mkl|10_mkl|13_mkl|14_mkl|15_mkl|4_openblas|5_openblas|11_openblas|16_openblas|15_openblas|14_openblas|13_openblas|12_openblas|10_openblas|9_openblas|8_openblas|7_openblas|6_openblas|12_mkl|11_mkl|8_mkl|7_mkl|6_mkl|5_mkl']

Package pathlib2 conflicts for:
pytest-cov -> pytest[version='>=4.6'] -> pathlib2[version='>=2.2.0']
pytest -> pathlib2[version='>=2.2.0']
ipywidgets==7.1.1 -> ipython[version='>=4.0.0'] -> pathlib2

Package hdf4 conflicts for:
hdf4==4.2.12
netcdf4==1.2.4 -> libnetcdf=4.4 -> hdf4[version='>=4.2.13,<4.2.14.0a0|>=4.2.13,<4.3.0a0']The following specifications were found to be incompatible with your CUDA driver:

  - feature:/linux-64::__cuda==10.2=0
  - feature:|@/linux-64::__cuda==10.2=0

Your installed CUDA driver is: 10.2

Installation Problem

Attempted installation of DeDop, following instructions at
http://dedop-core.readthedocs.io/en/latest/user_manual/um_setup.html

Trying on MacOSX 10.13, using Miniconda

The Miniconda download is a passive shell script. Needs an instruction to run the command “bash Miniconda3….” in terminal window (Download directory).
Default installation directory is under user’s home directory, changed to /Applications/miniconda3.
The conda installation was python 3.6, so first thing it did was revert to python 3.5
“git” command requires Xcode to be installed first, this is prompted for.
Dedop-core directory goes into top level of home directory, I moved it down a level.
Error after “dedop --help”:
```
Unable to proceed further
```

(dedop) Elliss-MacBook-Pro:dedop-core ellis$ dedop --help
Traceback (most recent call last):
File "/Applications/miniconda3/envs/dedop/bin/dedop", line 11, in
load_entry_point('dedop', 'console_scripts', 'dedop')()
File "/Applications/miniconda3/envs/dedop/lib/python3.5/site-packages/pkg_resources/init.py", line 572, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/Applications/miniconda3/envs/dedop/lib/python3.5/site-packages/pkg_resources/init.py", line 2755, in load_entry_point
return ep.load()
File "/Applications/miniconda3/envs/dedop/lib/python3.5/site-packages/pkg_resources/init.py", line 2408, in load
return self.resolve()
File "/Applications/miniconda3/envs/dedop/lib/python3.5/site-packages/pkg_resources/init.py", line 2414, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/Users/ellis/Processes/dedop-core/dedop/cli/main.py", line 23, in
from cate.util.cli import run_main, Command, SubCommandCommand, CommandError
ImportError: No module named 'cate'

Beam Angles

Summary

The Beam Angles algorithm computes the angles between the nadir direction and the direction from the burst location to each surface location observed by the burst.

Algorithm Description:

Find the surface location closest to the nadir direction, and select surface locations forwards and backwards from this location.
Compute the angles between the direction of each location and satellite's velocity vector.

Handle re-installation over an existing copy

Trying to install a new version over an existing copy lead to the following output:

DeDop will now be installed into this location:
/Users/djb/dedop

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below
[/Users/djb/dedop] >>>
/Users/djb/Applications/dedop
ERROR: File or directory already exists: /Users/djb/Applications/dedop

Ideally, the installer would detect the existing installation, and offer a mechanism for overwriting without requiring the user to remove the existing installation manually before installing.

The addition of DeDop to the path in .bash_profile is also repeated, even if it already exists.

Computation is slow when using an ROI filter

Expected behavior

the processor should run faster when using an ROI filter, since it does not have to process as much data

Actual behavior

The computation time is not much reduced

Steps to reproduce the issue

set an ROI in the CNF (min/max lat & lon)
process a file
the processing time is not reduce

Specifications

all platforms

Quick start guide issue?

I am trying to follow the quick start guide, and failing.

I installed DeDop using the shell file DeDop-0.5.2-MacOSX-x86_64.sh, in the default location.
The installation was smooth, and DeDop-Shell launches.
I can "add" one of the Pacific_Patch L1B files.
The file seems to be added to the default directory
~/.dedop/workspaces/default/inputs/CS_LTA__SIR1SAR_FR_20130109T132732_20130109T132816_C001.DBL.nc
When I "run" the file DeDop chokes. See the following screen dump.
I am guessing that I am misusing the software in my ignorance.

Begin Screen Dump.

Welcome to the DeDop Shell. Type dedop -h to get help.

(DeDop) $ dedop input add /Users/cray/Work2/DeDopData/CS_LTA__SIR1SAR_FR_20130109T132732_20130109T132816_C001.DBL.nc
adding inputs: done
one input added
(DeDop) $ dedop run
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: T0_h0_unit_conv_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: pitch_bias_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: yaw_bias_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: N_bursts_cycle_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: onboard_proc_sar_raw_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: pri_T0_unit_conv_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: cai_cor2_unit_conv_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: h0_cor2_unit_conv_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: i_sample_start_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: rfu_rx_gain_ground_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: roll_bias_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: fai_shift_number_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CHD file contains unknown parameter: pri_sar_chd
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: thermal_noise_first_range_bin_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: N_beams_sub_stack_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: step_avg_cal1_pulse_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: n_samples_fitting_rmc_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: zero_freq_sample_number_sar_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: thermal_noise_flag_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: num_lobes_int_cal1_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: min_num_contributing_looks_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: parameter_fitting_flag_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: sigma_z_seed_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: flag_l1bs_file_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: left_avoided_samples_cal2_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: zero_pad_fact_cal1_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: roughness_seed_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: zero_freq_sample_number_lrm_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: epoch_seed_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: flag_azimuth_weighting_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: num_samp_out_wfm_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: pu_seed_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: flag_cal1_source_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: sigma_alt_surf_th_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: thermal_noise_width_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: width_avg_cal1_pulse_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: flag_cal1_power_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: max_fitting_iterations_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: right_avoided_samples_cal2_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: n_samples_fitting_raw_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: decimation_fact_range_l1bs_cnf
UnknownParameterWarning(name, cls._id)
/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py:48: UnknownParameterWarning: CNF file contains unknown parameter: k_fact_int_cal1_cnf
UnknownParameterWarning(name, cls._id)
Traceback (most recent call last):
File "/Users/cray/dedop/bin/dedop", line 6, in
sys.exit(dedop.ui.cli.main())
File "/Users/cray/dedop/lib/python3.5/site-packages/dedop/ui/cli.py", line 1268, in main
status_and_message = args_obj.command_class().execute(args_obj)
File "/Users/cray/dedop/lib/python3.5/site-packages/dedop/ui/cli.py", line 255, in execute
skip_l1bs=skip_l1bs)
File "/Users/cray/dedop/lib/python3.5/site-packages/dedop/ui/cli.py", line 79, in new_l1b_processor
return L1BProcessor(name, cnf_file, cst_file, chd_file, output_dir, skip_l1bs)
File "/Users/cray/dedop/lib/python3.5/site-packages/dedop/proc/sar/processor.py", line 91, in init
self.gap_threshold = self.chd.bri_sar * 1.5
File "/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/characterization.py", line 87, in bri_sar
return 1. / self.brf_sar
File "/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_parameter.py", line 52, in get
value = self._retreive_value(instance)
File "/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_parameter.py", line 69, in _retreive_value
return instance[self.name]
File "/Users/cray/dedop/lib/python3.5/site-packages/dedop/conf/auxiliary_file_reader.py", line 72, in getitem
raise MissingParameterError(item, self._id)
dedop.conf.auxiliary_errors.MissingParameterError: CHD file does not contain a definition for parameter: brf_sar_chd
(DeDop) $ dedop output inspec L1B_default.nc
usage: dedop output [-h]
{clean,cl,list,ls,open,op,inspect,ins,compare,cmp} ...
dedop: dedop output: error: invalid choice: 'inspec' (choose from 'clean', 'cl', 'list', 'ls', 'open', 'op', 'inspect', 'ins', 'compare', 'cmp')

(DeDop) $ dedop output inspect L1B_default.nc
dedop: L1B product not found: /Users/cray/.dedop/workspaces/default/configs/default/outputs/L1B_default.nc
(DeDop) $

Extended output data format

Add new output data format called 'extended' (toggled with 'sentinel-3' in CNF file) which contains additional data & variables

Quick start guide: missing pyproj

Hi All,

I am having further difficulty following the quick start guide.

I did a clean install from source with Miniconda3 and specifying python version 3.5.
I was able to process L1B and L1Bs outputs but when I used the inspect command in dedop I get the following error in the jupyter window, which indicates that there is a missing file "pyproj"

Is it helpful that I am reporting these issues I am encountering while trying to get dedop running? Or would it be better if I waited until the project is more mature before giving feedback?

-Chris

ImportError Traceback (most recent call last)
in ()
----> 1 from dedop.ui.inspect import inspect_l1b_product
2 get_ipython().magic('matplotlib inline')

/Users/cray/dedop-core/dedop/ui/inspect.py in ()
9 import matplotlib.pyplot as plt
10 import numpy as np
---> 11 import pyproj
12 from IPython.display import display
13 from bokeh.models import ColumnDataSource, Circle

ImportError: No module named 'pyproj'

dedop / dedop-core Goto Github PK

dedop-core's Introduction

DeDop³

Contents

Installation using installer (recommended)

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> source activate dedop

To deactivate this environment, use:

> source deactivate dedop

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