Doc and tests

.coveragerc

@@ -2,6 +2,7 @@
 exclude_lines =
     pragma: no cover
 omit =
+    *__init__*
     *tests*
 show_missing = True
 

README.md

@@ -1,5 +1,4 @@
 [![Building Package](https://github.com/openalea-incubator/spice/actions/workflows/conda-package-build.yml/badge.svg)](https://github.com/openalea-incubator/spice/actions/workflows/conda-package-build.yml)
-[![Python Version](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue)](https://www.python.org/downloads/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![License: CeCILL-C](https://img.shields.io/badge/License--CeCILL-C-blue)](https://cecill.info/licences/Licence_CeCILL_V2-en.html)
 [![Anaconda-Server Badge](https://anaconda.org/openalea3/openalea.spice/badges/version.svg)](https://anaconda.org/openalea3/openalea.spice)

conda/meta.yaml

@@ -52,6 +52,7 @@ test:
     - openalea.spice.simulator
   requires:
     - openalea.plantgl
+    - openalea.lpy
     - pytest
   source_files:
     - tests/**

examples/python/obj-scene/main.py

@@ -1,9 +1,8 @@
-from datetime import datetime
 import random
-import sys
+from datetime import datetime
 from pathlib import Path
 
-from openalea.spice.libspice_core import *
+from openalea.spice import *
 
 if __name__ == "__main__":
     n_samples = 12
@@ -36,7 +35,8 @@
     print("Creating Scene..")
     scene = Scene()
     scene.loadModel(str(Path.home() / "models/Sponza/sponza.obj"))
-    scene.addPointLight(Vec3(0, -50, 0), 500, Vec3(1, 1, 1))
+    #scene.addPointLight(Vec3(0, -50, 0), 500, Vec3(1, 1, 1))
+    scene.addLight()
     scene.build()
 
     print("Done!")

src/openalea/spice/configuration.py

@@ -54,7 +54,7 @@ def read_file(self, filepath: Path):
 
         Parameters
         ----------
-        filepath: str
+        filepath: Path
             Name of the configuration file.
 
         """

src/openalea/spice/energy/calculate_energy.py

@@ -1,7 +1,7 @@
 import os
 
 # Objective of this module is counting the number of photon on plant/sensor
-# Resultat is located in this directory: ./results
+# Result is located in this directory: ./results
 
 
 def write_sensor_energy(n_sim, n_calibration, sensor_list, bands_spectre, filename):

src/openalea/spice/energy/correct_energy.py

@@ -93,13 +93,13 @@ def get_correct_energy_coeff(
     divided_spectral_range: range
         The section of the base spectral range used to run the simulation
     spec_file: str
-        The link to the file which contains the informations of the
+        The link to the file which contains the information of the
         heterogeneity of the spectrum
 
     Returns
     -------
     integrals: array
-        The list of the coefficents of energy's correction
+        The list of the coefficients of energy's correction
 
     """
 
@@ -161,7 +161,7 @@ def get_points_calibration(
     return points_calibration
 
 
-def get_calibaration_coefficient(energies, correction_ratios, points_calibration):
+def get_calibration_coefficient(energies, correction_ratios, points_calibration):
     """
     Calculate the coefficients used to calibrate the result of simulation
 
@@ -206,11 +206,11 @@ def get_calibaration_coefficient(energies, correction_ratios, points_calibration
     return coeff_calibration
 
 
-def calibrate_captor_energy(
+def calibrate_sensor_energy(
     energies, correction_ratios, points_calibration, coeffs_calibration
 ):
     """
-    Calibrate the captor energy from photons to Mmol / m2 / s
+    Calibrate the sensor energy from photons to Mmol / m2 / s
 
     Parameters
     ----------

src/openalea/spice/loader/load_plant.py

@@ -23,7 +23,7 @@
 # Data is located in this directory: ./assets
 
 
-def add_lpy_file_to_scene(scene, filename, t, tr2shmap, anchor, scale_factor):
+def add_lpy_file_to_scene(scene, filename, t, tr2shmap, anchor, scale_factor=1):
     """
     Adds the lpy mesh to the photonmapping scene.
 

src/openalea/spice/loader/load_sensor.py

@@ -120,83 +120,85 @@ def initVirtualDiskSensor(self, nor=(0, 0, 0), r=0, sensor_id=0):
             The id of sensor
 
         """
+        def createVirtualDisk(self):
+            """
+            Create geometry of circular sensor
+
+            Returns
+            -------
+            vertices: array
+                The vertices of sensor's geometry
+            normals: array
+                The normal vectors of each vertices in sensor's geometry
+            triangles: array
+                The triangles of sensor's geometry
+
+            """
+            vertices = []
+            normals = []
+            triangles = []
+
+            val = 3.14285 / 180
+            deltaAngle = 10
+            triangleCount = 0
+
+            vertices.append((self.xSite, self.ySite, self.zSite))
+            normals.append((self.xNormal, self.yNormal, self.zNormal))
+
+            if self.zNormal == 1:
+                x1 = self.radius * cos(0)
+                y1 = self.radius * sin(0)
+                z1 = 0
+            else:
+                x1 = self.radius * cos(0)
+                y1 = 0
+                z1 = self.radius * sin(0)
+
+            vertices.append((x1 + self.xSite, y1 + self.ySite, z1 + self.zSite))
+            normals.append((self.xNormal, self.yNormal, self.zNormal))
+
+            i = 0
+            while i < 360:
+                if self.zNormal == 1:
+                    x2 = self.radius * cos((i + deltaAngle) * val)
+                    y2 = self.radius * sin((i + deltaAngle) * val)
+                    z2 = 0
+                else:
+                    x2 = self.radius * cos((i + deltaAngle) * val)
+                    y2 = 0
+                    z2 = self.radius * sin((i + deltaAngle) * val)
+
+                vertices.append((x2 + self.xSite, y2 + self.ySite, z2 + self.zSite))
+                normals.append((self.xNormal, self.yNormal, self.zNormal))
+                triangles.append((triangleCount + 1, triangleCount + 2, 0))
+
+                triangleCount += 1
+                i += deltaAngle
+
+            sensor_shape = Shape(
+                TriangleSet(vertices, triangles, normals),
+                Material(
+                    name="Sensor",
+                    ambient=Color3(0),
+                    specular=Color3(0),
+                    shininess=1,
+                    transparency=0,
+                ),
+            )
+
+            self.shape = sensor_shape
+
         self.xNormal = nor[0]
         self.yNormal = nor[1]
         self.zNormal = nor[2]
         self.radius = r
         self.sensor_id = sensor_id
 
-        self.createVirtualDisk()
+        createVirtualDisk()
 
         return self
 
-    def createVirtualDisk(self):
-        """
-        Create geometry of circular sensor
-
-        Returns
-        -------
-        vertices: array
-            The vertices of sensor's geometry
-        normals: array
-            The normal vectors of each vertices in sensor's geometry
-        triangles: array
-            The triangles of sensor's geometry
-
-        """
-        vertices = []
-        normals = []
-        triangles = []
-
-        val = 3.14285 / 180
-        deltaAngle = 10
-        triangleCount = 0
-
-        vertices.append((self.xSite, self.ySite, self.zSite))
-        normals.append((self.xNormal, self.yNormal, self.zNormal))
-
-        if self.zNormal == 1:
-            x1 = self.radius * cos(0)
-            y1 = self.radius * sin(0)
-            z1 = 0
-        else:
-            x1 = self.radius * cos(0)
-            y1 = 0
-            z1 = self.radius * sin(0)
-
-        vertices.append((x1 + self.xSite, y1 + self.ySite, z1 + self.zSite))
-        normals.append((self.xNormal, self.yNormal, self.zNormal))
-
-        i = 0
-        while i < 360:
-            if self.zNormal == 1:
-                x2 = self.radius * cos((i + deltaAngle) * val)
-                y2 = self.radius * sin((i + deltaAngle) * val)
-                z2 = 0
-            else:
-                x2 = self.radius * cos((i + deltaAngle) * val)
-                y2 = 0
-                z2 = self.radius * sin((i + deltaAngle) * val)
-
-            vertices.append((x2 + self.xSite, y2 + self.ySite, z2 + self.zSite))
-            normals.append((self.xNormal, self.yNormal, self.zNormal))
-            triangles.append((triangleCount + 1, triangleCount + 2, 0))
-
-            triangleCount += 1
-            i += deltaAngle
-
-        sensor_shape = Shape(
-            TriangleSet(vertices, triangles, normals),
-            Material(
-                name="Sensor",
-                ambient=Color3(0),
-                specular=Color3(0),
-                shininess=1,
-                transparency=0,
-            ),
-        )
 
-        self.shape = sensor_shape
 
     def equal(self, xSite, ySite, zSite):
         """
@@ -213,8 +215,7 @@ def equal(self, xSite, ySite, zSite):
 
         Returns
         -------
-            True if equal
-            False if not equal
+            True if equal else False
 
         """
 
@@ -252,7 +253,7 @@ def getOpticalProperties(self):
         specular: float
             The specular
         trans: float
-            The tranparency
+            The transparency
         roughness: float
             The roughness
 

src/openalea/spice/simulator.py

@@ -509,7 +509,7 @@ def calculateCalibrationCoefficient(
                 points_calibration_file,
                 self.configuration.DIVIDED_SPECTRAL_RANGE,
             )
-            self.coeffs_calibration = correct_energy.get_calibaration_coefficient(
+            self.coeffs_calibration = correct_energy.get_calibration_coefficient(
                 self.N_sim_virtual_sensor, self.integrals, self.points_calibration
             )
             return True
@@ -626,6 +626,7 @@ def visualizeResults(self, mode="ipython", wavelength_index=0, colormap="jet"):
 
         if mode == "ipython":
             pgl.Viewer.display(self.scene_pgl)
+            return None
         elif mode == "oawidgets":
             from oawidgets.plantgl import PlantGL
             import k3d
@@ -650,6 +651,7 @@ def visualizeResults(self, mode="ipython", wavelength_index=0, colormap="jet"):
             return plot
         else:
             pgl.Viewer.display(self.scene_pgl)
+            return None
 
     def get_photons_per_triangles(self):
         """
@@ -770,7 +772,7 @@ def r():
                 ph_sc.add(sh)
             ph_sc.merge(self.scene_pgl)
             pgl.Viewer.display(ph_sc)
-
+            return None
         elif mode == "oawidgets":
             from oawidgets.plantgl import PlantGL
             import k3d
@@ -1143,6 +1145,8 @@ def setupRender(self, lookfrom=Vec3(0, 0, 0), lookat=Vec3(0, 0, 0), vfov=50.0):
             The position of the camera.
         lookat: Vec3
             The point where the camera is looking at
+        vfov: float
+            The vertical field of view of the camera
 
         """
         self.configuration.RENDERING = True
@@ -1226,6 +1230,8 @@ def initCameraRender(lookfrom=Vec3(0, 0, 0), lookat=Vec3(0, 0, 0), vfov=50.0):
             The position of the camera.
         lookat: Vec3
             The point where the camera is looking at
+        vfov: float
+            The vertical field of view of the camera
 
         Returns
         -------