Whean creatin g anew instance of AdelWheatDyn, we have to be able to define organ dimensions.
We also need to be able to access the dimensions tables for some parameters (sheath and internode diameter).

when executing code--python setup.py develop，prompt this

Function add_axe from mtg_editions does not compute nff parameter which causes a bug when using add_metamer function on the added tiller.

AdelWheatDyn should inherit from Adel instead AdelWheat to avoid R uneeded R dependency.
AdelWheatDyn only requires axeT and PhytoT

from alinea.adel.astk_interface import AdelWheat
from alinea.astk.Weather import sample_weather
seq, weather = sample_weather()
wdata = weather.get_weather(seq)
adel = AdelWheat(nsect=2)
g = adel.setup_canopy(100)
adel.grow(g, wdata)

Getting the error:

(adel) C:\Users\Personal\Desktop\OpenAlea research\adel\example>python test_AdelWheat.py
Traceback (most recent call last):
File "test_AdelWheat.py", line 1, in
from alinea.adel.astk_interface import AdelWheat
File "C:\Users\Personal\Desktop\OpenAlea research\adel\src\alinea\adel\astk_interface.py", line 6, in
from alinea.adel.AdelR import setAdel, RunAdel, genGeoAxe, checkAxeDyn, getAxeT,
File "C:\Users\Personal\Desktop\OpenAlea research\adel\src\alinea\adel\AdelR.py", line 23, in
import rpy2.robjects as robj
File "C:\Users\Personal.conda\envs\adel\lib\site-packages\rpy2\robjects_init_.py", line 16, in
import rpy2.rinterface as rinterface
File "C:\Users\Personal.conda\envs\adel\lib\site-packages\rpy2\rinterface_init_.py", line 92, in
from rpy2.rinterface._rinterface import (baseenv,
ImportError: DLL load failed: A dynamic link library (DLL) initialization routine failed.

From master branch convert Adel python 2 in python 3

• Convert using 2 to 3 packages

• Check all functionalities

Hi,

The attributes of an Adel object are not updated after loading a pickled MTG.

For instance, the script below,

from alinea.adel.astk_interface import AdelWheat

# Save MTG
adel_wheat_1 = AdelWheat(nplants=10)
g1 = adel_wheat_1.setup_canopy()
adel_wheat_1.save(g1)
print 'saved domain: ', adel_wheat_1.domain
print 'saved nplants: ', adel_wheat_1.nplants

# Loading MTG previously pickled 
adel_wheat_2 = AdelWheat()
g2 = adel_wheat_2.load(dir=r'~\adel_saved')
print 'loaded domain: ', adel_wheat_2.domain
print 'loaded nplants: ', adel_wheat_2.nplants

gives:

>>> 
'saved domain: ' ((-13.333333333333336, -7.5), (13.333333333333336, 7.5))
'saved nplants: ' 10
'loaded domain: ' ((-1.3333333333333335, -7.5), (1.3333333333333335, 7.5))
'loaded nplants: ' 1

Hi,
I'm having an issue when using AdelDress and dim_T in order to get a MTG with predefined blade dimensions. This may be due to an index error because of the metamer 0.
Here are two examples to illustrate the problem.

• The example below generates a MTG with only 3 metamers instead of 4 and with wrong dimensions for the blade of metamer 1.

from alinea.adel.dresser import blade_dimension, dimension_table, AdelDress

blades = blade_dimension(length=[0.0814, 0.0924, 0.0935, 0.001],
                         area=[9.73318E-4, 2.33465E-4, 8.2562E-4, 1E-6],
                         ntop=[4, 3, 2, 1])
dimT = dimension_table(blades)
adel = AdelDress(dimT=dimT, dim_unit='m', scene_unit='m', seed=1234)
g = adel.canopy()
g.display()

• The second example results in a KeyError in blade_dimension:

from alinea.adel.dresser import blade_dimension, dimension_table, AdelDress

blades = blade_dimension(length=[0.0814, 0.0924, 0.0935, 0.001],
                         area=[9.73318E-4, 2.33465E-4, 8.2562E-4, 1E-6],
                         ntop=[11, 10, 9, 8])

dimT = dimension_table(blades)
adel = AdelDress(dimT=dimT, dim_unit='m', scene_unit='m', seed=1234)
g = adel.canopy()
g.display()

It is currently impossible to conda install adel because the binaries/dependencies (like plantgl) don't exists (windows) or were build against an 8 year old glibc version (linux) which makes them impossible to run on any updated system.

I am currently building all dependencies manually and editing the meta.yaml in hope of getting this to work.
Should I have missed an easy solution for this issue I will happily close it.

Edit: this might be more of an issue with plantgl...

It would be nice to have a Python 2 branch

Dear, I enter the command as required, after the environment is configured, run the program, prompt this. But I have an R pack in my environment. How to solve.I've been operating for two days, and the environmental problems are still.

Sheath and lamina of leave number 8 are extending toward the ground. It seems it is not the case for internode 8.

Follow the installation instruction:

Installation with conda

Create an environment:

conda create -n adel -c openalea openalea.plantgl boost=1.66

(base) hwang@mac % conda create -n adel -c openalea openalea.plantgl boost=1.66
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
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                                                                          

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

Output in format: Requested package -> Available versions

Package boost conflicts for:
boost=1.66
openalea.plantgl -> cgal -> boost==1.57.0
openalea.plantgl -> boost

@christian34 : OK to move the repo to openalea org?
Need :

• conda packaging on openalea3
• rtfd
• tutorial

We would like to start our simulation with the full MTG : all leaves in all axis.
Then, we need a method to extract it.

Using add_metamer(), it seems like a new metamer has internodes and sheaths with diameters in centimer while all other values are in meter (length, area).

Error:

~\Documents\GitHub\adel\src\alinea\adel\newmtg.py in mtg_factory(parameters, metamer_factory, leaf_sectors, leaves, stand, axis_dynamics, add_elongation, topology, split, aborting_tiller_reduction, leaf_db)
    530             args.update({'split': split})
    531
--> 532             if args.get('HS_final') < args.get('nff'):
    533                 for what in (
    534                 'Ll', 'Lv', 'Lr', 'Lsen', 'L_shape', 'Lw_shape', 'Gl', 'Gv',

TypeError: '>' not supported between instances of 'numpy.ndarray' and 'numpy.str_'