Installing snappy - jpy problems

[maxlam64]

Hello,

I have been using the snappy library in Python without any problems until now, on a virtual machine. I have just been given a new desktop computer at work and can now work locally, but am now struggling to install Snappy.

I have setup Python with Anaconda 3, and followed the steps listed below:

• Installed Java JRE and JDK 8, setup the environement variables
• Installed SNAP
• Installed jpy manually, as previously mentionned on this forum
• Ran ./snappy-conf on my anaconda python path which yielded:

Done. The SNAP-Python interface is located in ‘/home/username/.snap/snap-python/snappy’

• Ran python setup.py install

When I start a python shell and type: import snappy , I get the following message:

Traceback (most recent call last):
File “”, line 1, in
File “/home/username/.snap/snap-python/snappy/init.py”, line 64, in
import jpy
ImportError: /home/username/.snap/snap-python/snappy/jpy.so: undefined symbol: _Py_ZeroStruct

Does anyone here know how I can sort this out?

Many thanks,

[forman]

Hi maxlam64,

Which Python version are you running. The missing symbol seems to indicate that it is a 3.5+. Unfortunately, snappy Python bindings are for 3.4 only. We are working on this issue right now.

Regards
Norman

[maxlam64]

Hi forman,

Thank you for your response. Indeed the problem was linked to the Python version. I have managed to complete the install in a Anaconda Virtual Env, using Python 3.4 .

All the best,

Maxim

[geoagr2003]

Hi Maxim, do you have some tips regarding the snappy installation in the Anaconda virtual environment ? I can’t have a successful install on my secondary py34 environment.

[maxlam64]

Hello,

I would suggest you take a look at this thread if you haven’t already:

Unable to install snappy - jpy problem?

Hi - I’m getting started with snappy and python and have been running into problems with the configuration. I’ve referenced the “Configure python to use SNAP” page and all posts on this forum - that have gotten me part way. . . but still not fully there. To start with - I’m using Python 3.6 on mac 10.12. I understand that snappy isn’t yet supported in this python version - but not sure if this is the reason I’m having problems with the install. If I open python3 and try to import snappy I ge…

[geoagr2003]

Hi Maxim,

Thanks for the answer.
I’ll have a look and come back with a comment over the solution and resolved issue if it will do the job :).

[geoagr2003]

Hi Maxim,

I tried installing snappy. My conclusion is that you can use snappy only if your start the script from the snappy interface folder. For example I have installed snappy on C:\Users…snappy\snappy-python, if I run the script anywhere on c:\ the script is working, if I move on D:\ then I can’t use snappy and the script is not working. I’m using an anaconda 3 py34 environment.
Do you have any other opinion ?

[maxlam64]

I didn’t run into this issue (but I’m on Linux). Probably @marpet can help you…

[marpet]

How have you integrated snappy into your anaconda environment?

Which of the steps have you done of the Configure Python
the section on the Configure Python to use the SNAP-Python (snappy) interface page. What kind of error do you get?
I’ve copied the snappy folder into the site-packages directory.
For me, it works also from another drive. See the image.

[geoagr2003]

Hi Marco,

First, thanks for not letting me down

Second, I’m resuming in the next rows the steps that I’ve used to enable snappy on Anaconda 3 (x64) .

I installed latest Apache Maven, Visual Studio from Microsoft and latest java client and jdk. Environment variables were configured:
User variables → Paths
C:\Program Files\apache\maven\bin

System variables
JAVA_HOME → C:\Program Files\Java\jdk1.8.0_172
JDK_HOME → JAVA_HOME

Full installed the ESA SNAP software without “Configure SNAP for use with Python” enabled;
Full updates for ESA SNAP;
The installation process created Environment variables → User variables → Paths → C:\Program Files\snap\bin

Full installed Anaconda 3 with Python 3.6

• In Anaconda prompt I created a new python 3.4 environment.
• activated python 3.4 new environment in anaconda 3;

While in py34 anaconda activated environment I’ve done the following steps:

• installing jpy from the C:\Users\The Specialist position by using git clone;

• from the same position I deployed: ‘snappy-conf C:\Anaconda3\envs\py34\python.exe’;
  cd /snappy;
  python setup.py install

• copied the C:\Users\The Specialist.snap\snap-python\snappy directory directly into the site-packages directory

• testing instalation from C:\Users\The Specialist position: python, import snappy → everything looks great and the my sentinel 2 project is working from this position
• the importing result looks like the following:

(py34) C:\Users\The Specialist>python
Python 3.4.5 | packaged by conda-forge | (default, Sep 8 2016, 14:36:52) [MSC v.1600 64 bit (AMD64)] on win32
Type “help”, “copyright”, “credits” or “license” for more information.

import snappy
INFO: org.esa.snap.python.gpf.PyOperatorSpi: Python operator ‘py_sambuca_snap_op’ registered (Python module: ‘sambuca_snap_op’, class: ‘sambuca_snap_op’, root: ‘C:\Users\The Specialist\AppData\Roaming\SNAP\modules\org-esa-sen2coral-sen2coral-inversion.jar’)
INFO: org.esa.snap.python.gpf.PyOperatorSpi: Python operator ‘S2RutOp’ registered (Python module: ‘s2_rut’, class: ‘S2RutOp’, root: ‘C:\Users\The Specialist\AppData\Roaming\SNAP\modules\org-esa-snap-snap-rut.jar’)
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters

• moving to D:\
• testing snappy
• python → import snappy => the module is not loading properly (see the bellow output) and the sentinel 2 script is not working
• I don’t have sys append or something similar in my script;
  (py34) C:\Users\The Specialist>d:

(py34) D:>python
Python 3.4.5 | packaged by conda-forge | (default, Sep 8 2016, 14:36:52) [MSC v.1600 64 bit (AMD64)] on win32
Type “help”, “copyright”, “credits” or “license” for more information.

import snappy
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters

You can see the difference also in the attached picture.

I don’t understand what should I do more in order to make it work.

[marpet]

Okay, now I see the problem and I can reproduce it.

In general your snappy is working and you could use the API. The problem is that some modules are not loaded. I see the same behaviour when I’m on my drive G. The S2RUT is not loaded in my case.
So it seems that modules installed later or updated are not considered.
I guess somewhere in snappy a wrong path is used. I’ll take look. (SNAP-929)

[marpet]

I’ve found the problem and fixed it. For the explanation see the issue SNAP-929

You can work around the problem by editing the __init__.py of snappy.
Go to method _get_nb_user_modules_dir() line 113.
And change it to:

def _get_nb_user_modules_dir():
    import platform
    from os.path import expanduser

    home_dir = expanduser('~')
    nb_user_dir = None
    if platform.system() == 'Windows':
        if home_dir:
            nb_user_dir = os.path.join(home_dir, 'AppData\\Roaming\\SNAP')
    else:
        if home_dir:
            nb_user_dir = os.path.join(home_dir, '.snap/system')

    if nb_user_dir:
        return os.path.join(nb_user_dir, 'modules')

    return None

Many thanks for the report @geoagr2003

[geoagr2003]

I will come back with a feedback tonight!

I forgot to mention that the reported issue was causing me also the necessity to write folders full paths in order to read/manipulate files from project location because I had to run the project from C:\ … .

Now, I hope to get my project working straight from its location.

Thanks again Marco!

Best regards,
George

[geoagr2003]

Hi Marco,

Just finished in dealing with the proposed solution.

Here are the steps that I pursued in having a clean and correct install of snappy, because there was an already installed version of the module (and I wanted to be sure that everything is ok).

First I uninstalled ESA SNAP, installed back without “Configure SNAP for use with Python” enabled.
2.
Run steps from ‘Configure Python to use the SNAP-Python (snappy) interface’ (https://senbox.atlassian.net/wiki/spaces/SNAP/pages/50855941/Configure+Python+to+use+the+SNAP-Python+snappy+interface) until the step:
Windows:
snappy-conf <python-exe> 3. After the step 2) I have operated the proposed changes inside __init__.py 4. After those changes I tried to permanently install snappy cd /snappy
$ setup.py install
No other folder copy was needed.

Wonderfull, now, the snappy module can be used from any location/disk (see the attached picture). All additionally installed modules are imported. Now I can run my sentinel 2 project from it’s location, no full paths are needed inside the developed modules

Thanks Marco!

George