Millet new by adamavip · Pull Request #106 · openalea/hydroroot

adamavip · 2026-02-16T08:50:20Z

I added a new implementation to build the millet root system as an MTG to architecture module
I renamed module turtle to turtle_millet and added visitor2 function to visualize the different root types (crown root are the thicker)
Add a notebook to simulate architectures for the lines 57 and 109

…sitor2 to turtle module to visualize MTGs

…cture

…ttps://github.com/adamavip/hydroroot into millet_new Merge remote branch origin/millet_new into millet_new

…cture

baugetfa

The notebook gives errors see my comments
I would change names with only '2' at the end because it is not very descriptive. But it is my point of view.
use conductance from hydroot not hydroroot.millet see comments in the ipynb and below.

baugetfa · 2026-02-20T10:30:25Z

doc/example/millet/Simulating_archicture.ipynb

at the cell Load diameter data for the different root types got the error

TypeError: readCSVFile() got an unexpected keyword argument 'delimiter'

Indeed in readCSVFile their is no delimiter. Just add it like that may be:

def readCSVFile(filename,delimiter=';'): """Read and extract data from a csv file, supposed that the data is stored in 2 columns. :param filename: string :returns: - data (array) - record array of (x, y) values, column headers recorded in dtype """ data = np.genfromtxt(filename,delimiter=delimiter,names=True) return data

I do not understand the figure with age. According to the heatmap the tips would be the oldest but it is not the case the tips are the youngest part of the root. So I think I misunderstand something: either it is the time of appearance so it is not the age or the heatmap is inversed.

from openalea.hydroroot.millet import conductance as conductance_millet; reload(conductance)

got

NameError: name 'conductance' is not defined

Remove ; reload(conductance)

Compute K for the lines missing s in view()

s = mtg_scene(g109, prop_cmap='K') view()

compute radial conducances
use hydroroot.conductance.fit_property_from_spline instead of hydroroot.millet.conductance it is buggy.

from openalea.hydroroot import conductance g57 = conductance.fit_property_from_spline(g57, radial_law57, 'position', 'k0') g57 = conductance.compute_k(g57, k0='k0') g109 = conductance.fit_property_from_spline(g109, radial_law109, 'position', 'k0') g109 = conductance.compute_k(g109, k0='k0')

TypeError: readCSVFile() got an unexpected keyword argument 'delimiter'
I will use pandas.read_csv directly then destructure x and y

Age calculation:
I think the problem comes from the fact that we fixing the passed to leaf vertices: if g.is_leaf(v):
age[v] = sr_age
@pradal can we for every axis, the maximum subtracted from the age of each vertex, so that tips become the youngest

from openalea.hydroroot.millet import conductance as conductance_millet; reload(conductance)
This is a lapsus should be reload(conductance_millet_

Lapus when using view, should be view(s)

baugetfa · 2026-02-20T10:32:29Z

src/openalea/hydroroot/millet/architecture.py

+from openalea.mtg.mtg import fat_mtg
+
+
+def millet_mtg2(


change name.

added 2 as a new implementation comparing the old one but can use another name

Proposal:
millet_mtg2 -> generate_millet or millet

baugetfa · 2026-02-20T10:34:58Z

src/openalea/hydroroot/millet/conductance.py


    #spline = UnivariateSpline(x, y, s=s)
    keys = g.property(prop_in).keys()
    x_values = np.array(g.property(prop_in).values())


This is buggy. It gives a dict should be x_values = np.array(list(g.property(prop_in).values())) but use instead hydroroot.conductance.fit_property_from_spline and delete this duplicate

No. values() returns an iterable.
But I agree that we have to reuse conductance from hydroroot.

@baugetfa You are right!
@adamavip Delete this function and use hydroroot.conductance one

baugetfa · 2026-02-20T10:35:47Z

src/openalea/hydroroot/millet/law.py

    law = f
    return law

+def diameter_law2(data_xy, function=None, plot= True):


change name. '2' is not descriptive

'2' is used just to design a second implementation but agreed not very descriptive

Make the opposite if you think you need two functions.
Otherelse, just keep one...

baugetfa · 2026-02-20T10:37:49Z

src/openalea/hydroroot/millet/law.py

 # ************** Here we define evolution diameter laws of different root types************************

+
+def compute_diameter_from_laws(g,


cannot we have either diameter or radius not both as MTG properties. This is the same information and it avoid to have a function like compute_radius_from_diameter ?

the problem is we estimated the diameter from the evolution laws, then consequently calculated the radius afterwards

Yes but diameter and radius is linked. So just compute radius directly (just /2).

baugetfa · 2026-02-20T10:39:00Z

src/openalea/hydroroot/millet/Simulating_archicture.ipynb

we should have a notebook in src I think

yes shouldn't

baugetfa · 2026-02-20T10:40:42Z

src/openalea/hydroroot/conductance.py


 def compute_k(g, k0 = 300.):
-    """Compute the radial conductance k (:math:`10^{-9}\ m.s^{-1}.MPa^{-1}`) of each vertex of the MTG.
+    r"""Compute the radial conductance k (:math:`10^{-9}\ m.s^{-1}.MPa^{-1}`) of each vertex of the MTG.


Their is an error here that I corrected it is in fact m^4.s^{-1}.MPa^{-1}
The 'r' is not neccessary their is not bug in the doc.

I add the rstring due to a warning for escape charater...

NDOUR added 2 commits February 16, 2026 11:38

added new implementation to generate the root architecture and add vi…

f5a5a5f

…sitor2 to turtle module to visualize MTGs

added new implementation to generate the root architecture and add vi…

a7d67d5

…sitor2 to turtle module to visualize MTGs

pradal requested review from baugetfa and pradal February 16, 2026 13:35

pradal and others added 10 commits February 17, 2026 08:46

Modify docstring for math

f0b49ee

Remove unused UnivariateSpine import

9c501ce

Modify import to run code

93e9011

update notebook

fc91941

update

a7113b2

updating architecture simulation and calculation of hydraulic archite…

5595f2c

…cture

updating architecture simulation and calculation of hydraulic archite…

2972b84

…cture

updating architecture simulation and calculation of hydraulic archite…

5f4f046

…cture

Mgit push --set-upstream origin millet_newerge branch 'millet_new' of h…

3e8ae94

…ttps://github.com/adamavip/hydroroot into millet_new Merge remote branch origin/millet_new into millet_new

updating architecture simulation and calculation of hydraulic archite…

1edc5e2

…cture

baugetfa requested changes Feb 20, 2026

View reviewed changes

Merge branch 'main' into millet_new

2233672

		# ************ Here we define evolution diameter laws of different root types**********************


		def compute_diameter_from_laws(g,

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adamavip commented Feb 16, 2026

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baugetfa Feb 20, 2026 •

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