From daa0c67cf6de8ebea7c2f2e2fdde8a3cd2d747c4 Mon Sep 17 00:00:00 2001 From: rbarillot Date: Mon, 18 Oct 2021 15:07:33 +0200 Subject: [PATCH] - reformat caribu_facade.py to handle calculations at primitive scale - update Vegetative_stages/main.py with new farquhar options - update NEMA examples with new farquhar options --- doc/conf.py | 260 ------------- doc/index.rst | 62 --- doc/ref.rst | 64 ---- doc/user.rst | 72 ---- example/NEMA/Multi_script_launcher.py | 12 + example/NEMA/NEMA_H0/main.py | 3 +- example/NEMA/NEMA_H15/main.py | 3 +- example/NEMA/NEMA_H3/main.py | 3 +- example/Vegetative_stages/main.py | 2 +- fspmwheat/caribu_facade.py | 67 +++- test/outputs/desired_axes_outputs.csv | 46 +-- test/outputs/desired_elements_outputs.csv | 360 ++++++++--------- test/outputs/desired_hiddenzones_outputs.csv | 384 +++++++++---------- test/outputs/desired_organs_outputs.csv | 94 ++--- test/outputs/desired_soils_outputs.csv | 46 +-- 15 files changed, 534 insertions(+), 944 deletions(-) delete mode 100644 doc/conf.py delete mode 100644 doc/index.rst delete mode 100644 doc/ref.rst delete mode 100644 doc/user.rst create mode 100644 example/NEMA/Multi_script_launcher.py diff --git a/doc/conf.py b/doc/conf.py deleted file mode 100644 index af944c5..0000000 --- a/doc/conf.py +++ /dev/null @@ -1,260 +0,0 @@ -# -*- coding: latin-1 -*- -# -# CN-Wheat documentation build configuration file, created by -# sphinx-quickstart on Fri Sep 12 17:31:09 2014. -# -# This file is execfile()d with the current directory set to its containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -""" - Information about this versioned file: - $LastChangedBy: rbarillot $ - $LastChangedDate: 2015-03-16 12:08:39 +0100 (lun., 16 mars 2015) $ - $LastChangedRevision: 139 $ - $URL: https://subversion.renater.fr/cn-wheat/trunk/doc/conf.py $ - $Id: conf.py 139 2015-03-16 11:08:39Z rbarillot $ -""" - -import sys, os - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -#sys.path.insert(0, os.path.abspath('.')) - -# -- General configuration ----------------------------------------------------- - -# If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be extensions -# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'sphinx.ext.intersphinx'] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix of source filenames. -source_suffix = '.rst' - -# The encoding of source files. -#source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = u'CN-Wheat' -copyright = u'2014, C.Chambon and R.Barillot' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = '0.0.1' -# The full version, including alpha/beta/rc tags. -release = '0.0.1' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -#language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -#today = '' -# Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = ['_build'] - -# The reST default role (used for this markup: `text`) to use for all documents. -#default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -#add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -#show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] - - -# -- Options for HTML output --------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -html_theme = 'default' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -#html_theme_options = {} - -# Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -#html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -#html_logo = None - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -#html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -#html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -#html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -#html_additional_pages = {} - -# If false, no module index is generated. -#html_domain_indices = True - -# If false, no index is generated. -#html_use_index = True - -# If true, the index is split into individual pages for each letter. -#html_split_index = False - -# If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -#html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -#html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None - -# Output file base name for HTML help builder. -htmlhelp_basename = 'CN-Wheatdoc' - - -# -- Options for LaTeX output -------------------------------------------------- - -latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass [howto/manual]). -latex_documents = [ - ('index', 'CN-Wheat.tex', u'CN-Wheat Documentation', - u'C.Chambon and R.Barillot', 'manual'), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False - -# Documents to append as an appendix to all manuals. -#latex_appendices = [] - -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output -------------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'cn-wheat', u'CN-Wheat Documentation', - [u'C.Chambon and R.Barillot'], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------------ - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ('index', 'CN-Wheat', u'CN-Wheat Documentation', - u'C.Chambon and R.Barillot', 'CN-Wheat', 'Model of CN distribution for wheat', - 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] - -# If false, no module index is generated. -#texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' - -intersphinx_mapping = {'python': ('http://docs.python.org/2', None), - 'pandas': ('http://pandas.pydata.org/pandas-docs/stable/', None), - 'numpy': ('http://docs.scipy.org/doc/numpy/', None), - 'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None), - 'matplotlib': ('http://matplotlib.sourceforge.net/', None) - } - -autodoc_member_order = 'bysource' diff --git a/doc/index.rst b/doc/index.rst deleted file mode 100644 index 0eb6e3a..0000000 --- a/doc/index.rst +++ /dev/null @@ -1,62 +0,0 @@ - -.. _cnwheat: - -.. module:: cnwheat - -CN-Wheat documentation -###################### - -Module description -================== - -.. sidebar:: Summary - - :Version: |version| - :Release: |release| - :Date: |today| - :Author: See `Authors`_ section - :ChangeLog: See `ChangeLog`_ section - -.. topic:: Overview - - CN-Wheat is a model of CN distribution for wheat. - - -Documentation -============= - -.. toctree:: - :maxdepth: 2 - - User Guide - Reference Guide - - -Authors -======= - -.. include:: ../AUTHORS - - -ChangeLog -========= - -.. include:: ../CHANGES - - -License -======= - -|cnwheat| is released under TODO License. - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - - -.. |cnwheat| replace:: :mod:`cnwheat` - diff --git a/doc/ref.rst b/doc/ref.rst deleted file mode 100644 index b76565d..0000000 --- a/doc/ref.rst +++ /dev/null @@ -1,64 +0,0 @@ -.. |cnwheat| replace:: :mod:`cnwheat` - -.. _cnwheat_reference: - -Reference guide -################# - -This manual details, for each module of |cnwheat|, -the functions and objects included in |cnwheat|, -describing what they are and what they do. - -.. contents:: - -.. currentmodule:: cnwheat.__init__ - -|cnwheat| package -********************************************************* - -.. automodule:: cnwheat - :members: - :undoc-members: - :show-inheritance: - :synopsis: - - -:mod:`cnwheat.simulation` module -********************************************************* - -.. automodule:: cnwheat.simulation - :members: - :undoc-members: - :show-inheritance: - :synopsis: - - -:mod:`cnwheat.model` module -********************************************************* - -.. automodule:: cnwheat.model - :members: - :undoc-members: - :show-inheritance: - :synopsis: - - -:mod:`cnwheat.parameters` module -********************************************************* - -.. automodule:: cnwheat.parameters - :members: - :undoc-members: - :show-inheritance: - :synopsis: - - -:mod:`cnwheat.tools` module -********************************************************* - -.. automodule:: cnwheat.tools - :members: - :undoc-members: - :show-inheritance: - :synopsis: - diff --git a/doc/user.rst b/doc/user.rst deleted file mode 100644 index f69baa0..0000000 --- a/doc/user.rst +++ /dev/null @@ -1,72 +0,0 @@ - -.. _cnwheat_user: - -CN-Wheat User Guide -################### - -.. contents:: - -Introduction -============ - -This is the documentation for CN-Wheat, a CN distribution model for wheat. - -Prerequisites -------------- - -CN-Wheat needs at least Python_ (2.7 or newer) to run, as well as the -NumPy_ (1.7.2 or newer), SciPy_ (0.12.1 or newer), Pandas_ (0.14.0 or newer), -Matplotlib_ (1.3.1 or newer) and Respi-Wheat_ libraries. -CN-Wheat has not been tested with **Python 3**. - -.. _Python: http://www.python.org/ -.. _NumPy: http://www.numpy.org/ -.. _SciPy: http://www.scipy.org/ -.. _Pandas: http://pandas.pydata.org/ -.. _Matplotlib: http://matplotlib.org/ -.. _Respi-Wheat: https://sourcesup.renater.fr/projects/respi-wheat/ - - -Usage ------ - -See :ref:`getting_started` for an introduction. - - -Installing -========== - -First get the sources using ``svn``:: - - svn checkout https://subversion.renater.fr/cn-wheat - -This creates the directory ``cn-wheat``. - -Then, in the directory ``cn-wheat``, run:: - - python setup.py install - -Or, to install in develop mode, run:: - - python setup.py develop - - -.. _getting_started: - -Getting started -=============== - -TODO - - -Inputs of CN-Wheat -================== - -TODO - - -Outputs of CN-Wheat -=================== - -TODO - diff --git a/example/NEMA/Multi_script_launcher.py b/example/NEMA/Multi_script_launcher.py new file mode 100644 index 0000000..c0c9d4d --- /dev/null +++ b/example/NEMA/Multi_script_launcher.py @@ -0,0 +1,12 @@ +from subprocess import Popen + + +def multi_script_launcher(): + commands = ['cd NEMA_H0 && python main.py', 'cd NEMA_H3 && python main.py', 'cd NEMA_H15 && python main.py'] + processes = [Popen(cmd, shell=True) for cmd in commands] + for p in processes: + p.wait() + + +if __name__ == '__main__': + multi_script_launcher() diff --git a/example/NEMA/NEMA_H0/main.py b/example/NEMA/NEMA_H0/main.py index 942fa07..971bbf7 100644 --- a/example/NEMA/NEMA_H0/main.py +++ b/example/NEMA/NEMA_H0/main.py @@ -214,7 +214,8 @@ def main(stop_time, run_simu=True, make_graphs=True): # farquharwheat farquharwheat_elements_inputs_t0 = pd.read_csv(FARQUHARWHEAT_INPUTS_FILEPATH) farquharwheat_axes_inputs_t0 = pd.read_csv(FARQUHARWHEAT_AXES_INPUTS_FILEPATH) - update_parameters_farquharwheat = {'MODEL_VERSION': 'Barillot2016'} # Use the initial version of the photosynthesis sub-model (as in Barillot et al. 2016, and in Gauthier et al. 2020) + # Use the initial version of the photosynthesis sub-model (as in Barillot et al. 2016, and in Gauthier et al. 2020) + update_parameters_farquharwheat = {'SurfacicProteins': False, 'NSC_Retroinhibition': False} farquharwheat_facade_ = farquharwheat_facade.FarquharWheatFacade(g, farquharwheat_elements_inputs_t0, diff --git a/example/NEMA/NEMA_H15/main.py b/example/NEMA/NEMA_H15/main.py index fc0f3aa..e3236d8 100644 --- a/example/NEMA/NEMA_H15/main.py +++ b/example/NEMA/NEMA_H15/main.py @@ -214,7 +214,8 @@ def main(stop_time, run_simu=True, make_graphs=True): # farquharwheat farquharwheat_elements_inputs_t0 = pd.read_csv(FARQUHARWHEAT_INPUTS_FILEPATH) farquharwheat_axes_inputs_t0 = pd.read_csv(FARQUHARWHEAT_AXES_INPUTS_FILEPATH) - update_parameters_farquharwheat = {'MODEL_VERSION': 'Barillot2016'} # Use the initial version of the photosynthesis sub-model (as in Barillot et al. 2016, and in Gauthier et al. 2020) + # Use the initial version of the photosynthesis sub-model (as in Barillot et al. 2016, and in Gauthier et al. 2020) + update_parameters_farquharwheat = {'SurfacicProteins': False, 'NSC_Retroinhibition': False} farquharwheat_facade_ = farquharwheat_facade.FarquharWheatFacade(g, farquharwheat_elements_inputs_t0, diff --git a/example/NEMA/NEMA_H3/main.py b/example/NEMA/NEMA_H3/main.py index b8c2be4..134ed0b 100644 --- a/example/NEMA/NEMA_H3/main.py +++ b/example/NEMA/NEMA_H3/main.py @@ -214,7 +214,8 @@ def main(stop_time, run_simu=True, make_graphs=True): # farquharwheat farquharwheat_elements_inputs_t0 = pd.read_csv(FARQUHARWHEAT_INPUTS_FILEPATH) farquharwheat_axes_inputs_t0 = pd.read_csv(FARQUHARWHEAT_AXES_INPUTS_FILEPATH) - update_parameters_farquharwheat = {'MODEL_VERSION': 'Barillot2016'} # Use the initial version of the photosynthesis sub-model (as in Barillot et al. 2016, and in Gauthier et al. 2020) + # Use the initial version of the photosynthesis sub-model (as in Barillot et al. 2016, and in Gauthier et al. 2020) + update_parameters_farquharwheat = {'SurfacicProteins': False, 'NSC_Retroinhibition': False} farquharwheat_facade_ = farquharwheat_facade.FarquharWheatFacade(g, farquharwheat_elements_inputs_t0, diff --git a/example/Vegetative_stages/main.py b/example/Vegetative_stages/main.py index 77fe34a..b881309 100644 --- a/example/Vegetative_stages/main.py +++ b/example/Vegetative_stages/main.py @@ -323,7 +323,7 @@ def main(simulation_length, forced_start_time=0, run_simu=True, run_postprocessi [i for i in farquharwheat_facade.converter.FARQUHARWHEAT_AXES_INPUTS if i in inputs_dataframes[AXES_INITIAL_STATE_FILENAME].columns]].copy() # Use the initial version of the photosynthesis sub-model (as in Barillot et al. 2016, and in Gauthier et al. 2020) - update_parameters_farquharwheat = {'MODEL_VERSION': 'Barillot2016'} + update_parameters_farquharwheat = {'SurfacicProteins': False, 'NSC_Retroinhibition': False} # Facade initialisation farquharwheat_facade_ = farquharwheat_facade.FarquharWheatFacade(g, diff --git a/fspmwheat/caribu_facade.py b/fspmwheat/caribu_facade.py index c799f5d..5103142 100755 --- a/fspmwheat/caribu_facade.py +++ b/fspmwheat/caribu_facade.py @@ -29,7 +29,7 @@ SHARED_ELEMENTS_INPUTS_OUTPUTS_INDEXES = ['plant', 'axis', 'metamer', 'organ', 'element'] #: the outputs of Caribu -CARIBU_OUTPUTS = ['PARa', 'Erel'] +CARIBU_OUTPUTS = ['PARa', 'Erel', 'PARa_prim', 'Erel_prim'] class CaribuFacade(object): @@ -59,7 +59,7 @@ def __init__(self, self._update_shared_df = update_shared_df def run(self, run_caribu, sun_sky_option='mix', energy=1, DOY=1, hourTU=12, latitude=48.85, diffuse_model='soc', azimuts=4, zenits=5, heterogeneous_canopy=False, - plant_density=250., inter_row=0.15, update_shared_df=None): + plant_density=250., inter_row=0.15, update_shared_df=None, prim_scale=False): """ Run the model and update the MTG and the dataframes shared between all models. @@ -76,33 +76,56 @@ def run(self, run_caribu, sun_sky_option='mix', energy=1, DOY=1, hourTU=12, lati :param float plant_density: Number of plant per m2 in the stand (plant m-2). :param float inter_row: Inter-row spacing in the stand (m). :param bool update_shared_df: if 'True', update the shared dataframes at this time step. + :param bool prim_scale: If True, light distribution output at primitive scale, if not at organ scale """ - c_scene_sky, c_scene_sun, Erel_input = self._initialize_model(run_caribu, 1, diffuse_model, azimuts, zenits, DOY, hourTU, latitude, heterogeneous_canopy, plant_density, inter_row) - + c_scene_sky, c_scene_sun, Erel_input, Erel_input_prim = self._initialize_model(run_caribu, + 1, + diffuse_model, + azimuts, + zenits, + DOY, + hourTU, + latitude, + heterogeneous_canopy, + plant_density, + inter_row) + outputs = {} if run_caribu: #: Diffuse light if sun_sky_option == 'sky': - _, aggregated_sky = c_scene_sky.run(direct=True, infinite=True) + raw, aggregated_sky = c_scene_sky.run(direct=True, infinite=True) Erel_sky = aggregated_sky['par']['Eabs'] #: Erel is the relative surfacic absorbed energy per organ PARa_sky = {k: v * energy for k, v in Erel_sky.items()} Erel_output = Erel_sky PARa_output = PARa_sky + # Primitive scale + if prim_scale: + Erel_prim = raw['par']['Eabs'] + raw_Eabs_abs = {k: [Eabs * energy for Eabs in raw['par']['Eabs'][k]] for k in raw['par']['Eabs']} + outputs.update({'Erel_prim': Erel_prim, 'PARa_prim': raw_Eabs_abs, 'area_prim': raw['par']['area']}) + #: Direct light elif sun_sky_option == 'sun': - _, aggregated_sun = c_scene_sun.run(direct=True, infinite=True) + raw, aggregated_sun = c_scene_sun.run(direct=True, infinite=True) Erel_sun = aggregated_sun['par']['Eabs'] #: Erel is the relative surfacic absorbed energy per organ PARa_sun = {k: v * energy for k, v in Erel_sun.items()} Erel_output = Erel_sun PARa_output = PARa_sun + # Primitive scale + if prim_scale: + Erel_prim = raw['par']['Eabs'] + raw_Eabs_abs = {k: [Eabs * energy for Eabs in raw['par']['Eabs'][k]] for k in raw['par']['Eabs']} + outputs.update({'Erel_prim': Erel_prim, 'PARa_prim': raw_Eabs_abs, 'area_prim': raw['par']['area']}) + #: Mix sky-Sun elif sun_sky_option == 'mix': #: Diffuse - _, aggregated_sky = c_scene_sky.run(direct=True, infinite=True) + raw_sky, aggregated_sky = c_scene_sky.run(direct=True, infinite=True) Erel_sky = aggregated_sky['par']['Eabs'] #: Direct - _, aggregated_sun = c_scene_sun.run(direct=True, infinite=True) + raw_sun, aggregated_sun = c_scene_sun.run(direct=True, infinite=True) Erel_sun = aggregated_sun['par']['Eabs'] #: Spitters's model estimating for the diffuse:direct ratio @@ -111,18 +134,27 @@ def run(self, run_caribu, sun_sky_option='mix', energy=1, DOY=1, hourTU=12, lati Erel = {} for element_id, Erel_value in Erel_sky.items(): Erel[element_id] = RdRs * Erel_value + (1 - RdRs) * Erel_sun[element_id] + Erel_output = Erel PARa_output = {k: v * energy for k, v in Erel_output.items()} + # Primitive scale + if prim_scale: + raise ValueError("prim_scale not yet implemented for mix sun_sky_option.") + else: raise ValueError("Unknown sun_sky_option : can be either 'mix', 'sun' or 'sky'.") # Ouputs - outputs = {'PARa': PARa_output, 'Erel': Erel_output} - + outputs.update({'PARa': PARa_output, 'Erel': Erel_output}) else: PARa_output = {k: v * energy for k, v in Erel_input.items()} - outputs = {'PARa': PARa_output} + raw_Eabs_abs = {k: [Eabs * energy for Eabs in Erel_input_prim[k]] for k in Erel_input_prim} + outputs.update({'PARa': PARa_output}) + + # Primitive scale + if prim_scale: + outputs.update({'PARa_prim': raw_Eabs_abs}) # Updates self.update_shared_MTG(outputs) @@ -143,10 +175,10 @@ def _initialize_model(self, run_caribu, energy, diffuse_model, azimuts, zenits, :param float latitude: latitude to be used for solar sources (°) :param bool heterogeneous_canopy: Whether to create a duplicated heterogeneous canopy from the initial mtg. - :return: A tuple of Caribu scenes instantiated for sky and sun sources, respectively, and a dictionary with Erel value per vertex id. - :rtype: (CaribuScene, CaribuScene, dict) + :return: A tuple of Caribu scenes instantiated for sky and sun sources, respectively, and two dictionaries with Erel value per vertex id and per primitive. + :rtype: (CaribuScene, CaribuScene, dict, dict) """ - c_scene_sky, c_scene_sun, Erel = None, None, None + c_scene_sky, c_scene_sun, Erel, Erel_prim = None, None, None, None if run_caribu: @@ -190,8 +222,9 @@ def _initialize_model(self, run_caribu, energy, diffuse_model, azimuts, zenits, else: Erel = self._shared_mtg.property('Erel') + Erel_prim = self._shared_mtg.property('Erel_prim') - return c_scene_sky, c_scene_sun, Erel + return c_scene_sky, c_scene_sun, Erel, Erel_prim def _create_heterogeneous_canopy(self, nplants=50, var_plant_position=0.03, var_leaf_inclination=0.157, var_leaf_azimut=1.57, var_stem_azimut=0.157, plant_density=250, inter_row=0.15): @@ -266,8 +299,8 @@ def _create_heterogeneous_canopy(self, nplants=50, var_plant_position=0.03, var_ anchor_point = self._shared_mtg.get_vertex_property(shp.id)['anchor_point'] trans_to_origin = plantgl.Translated(-anchor_point, shp.geometry) # Rotation variability - azimut = self._alea_canopy.loc[(self._alea_canopy.pos == position_number) & (self._alea_canopy.vid == shp.id), 'azimut_leaf'].values[0] # random.uniform(-var_leaf_azimut, var_leaf_azimut) - inclination = self._alea_canopy.loc[(self._alea_canopy.pos == position_number) & (self._alea_canopy.vid == shp.id), 'inclination_leaf'].values[0] # random.uniform(-var_leaf_inclination, var_leaf_inclination) + azimut = self._alea_canopy.loc[(self._alea_canopy.pos == position_number) & (self._alea_canopy.vid == shp.id), 'azimut_leaf'].values[0] + inclination = self._alea_canopy.loc[(self._alea_canopy.pos == position_number) & (self._alea_canopy.vid == shp.id), 'inclination_leaf'].values[0] rotated_geometry = plantgl.EulerRotated(azimut, inclination, 0, trans_to_origin) # Restore leaf base at initial anchor point translated_geometry = plantgl.Translated(anchor_point, rotated_geometry) diff --git a/test/outputs/desired_axes_outputs.csv b/test/outputs/desired_axes_outputs.csv index 931a1c5..25c206a 100644 --- a/test/outputs/desired_axes_outputs.csv +++ b/test/outputs/desired_axes_outputs.csv @@ -1,25 +1,25 @@ mstruct,senesced_mstruct,C_exudated,sum_respi_shoot,sum_respi_roots 0.05410729300000001,0.0,0.0,0.0,0.001 -0.0542044957733635,0.0,0.0,0.45555180783346416,0.25108975954843304 -0.05424677531552684,0.0,0.0,0.42042563415911455,0.226153389804335 -0.05429492372753708,0.0,0.0,0.4300475318803062,0.2345945129045325 -0.05434065506326862,0.0,0.0,0.3324817406537266,0.22506217168143547 -0.05438437307676718,0.0,0.0,0.33499762857393767,0.2173011247478538 -0.05442676420890078,0.0,0.0,0.3407958587287173,0.21186562472352746 -0.054468369099669574,0.0,0.0,0.34494525599395837,0.20830671965825098 -0.054509593344619287,0.0,0.0,0.32149142289806487,0.20610539890068488 -0.05455051049853427,0.0,5.111148321056147e-05,0.3209094032566178,0.20412884200819298 -0.05459128782658103,0.0,0.04152811699944113,0.33183341350399265,0.20269804629112106 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+0.055122335329654104,0.0,0.27132802573549586,0.392722180629173,0.20582970473372963 diff --git a/test/outputs/desired_elements_outputs.csv b/test/outputs/desired_elements_outputs.csv index 897fe6e..73d9730 100644 --- a/test/outputs/desired_elements_outputs.csv +++ b/test/outputs/desired_elements_outputs.csv @@ -1,194 +1,194 @@ Ag,Nstruct,Tr,Ts,green_area,is_growing,mstruct,senesced_mstruct,amino_acids,cytokinins,fructan,nitrates,proteins,starch,sucrose,triosesP -9.881282504136573,2.05e-05,0.9978350094156574,10.334752441513988,0.00019533286142782728,False,0.004106768,0.0,1.69,0.349075266,0.0,0.0,16.93543686,0.0,24.15745785,0.0 -0.7663880496470791,8.55e-06,0.3442461794496808,8.646067477409963,0.0002686061718819273,False,0.0017100000000000001,0.0,0.20231970100000002,0.04104,0.0,0.0,2.023197008,0.0,10.05882353,0.0 -10.517828104761,2.42e-05,0.9338868381027845,9.961615458791826,0.00024106933629873322,False,0.004837643,0.0,2.36,0.48860194100000004,0.0,0.0,23.63639357,0.0,28.4567234,0.0 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