Merge pull request #25 from pradal/gitign

Add .gitignore file

.gitignore

@@ -0,0 +1,97 @@
+# {# pkglts, github
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# pkglts files
+.pkglts/info.log*
+
+# Packages
+*.egg
+*.egg-info
+.eggs
+.Python
+*.pth
+dist/
+build/
+env/
+downloads/
+eggs/
+parts/
+bin/
+var/
+sdist/
+develop-eggs/
+.installed.cfg
+lib/
+lib64/
+
+# editors
+.idea/
+
+# Vim files
+*.swp
+*.*~
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+.settings
+
+
+# C extensions
+*.so
+*.dll
+*.dylib
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+
+# Compiled Object files
+*.os
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+.amlog
+.sconsign.dblite
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# PyBuilder
+target/
+
+# jupyter notebooks
+.ipynb_checkpoints/
+
+# svn
+.svn
+.cache/
+
+# coverage
+.coverage
+
+# sphinx autogen file
+doc/_dvlpt/
+
+
+# #}
+
+# user custom filters
+
+# Mac
+.DS_Store

example/test_newmtg.py

@@ -4,6 +4,9 @@
 from alinea.adel.AdelR import devCsv,setAdel,RunAdel,genGeoLeaf,genGeoAxe
 import alinea.adel.fitting as fitting
 
+import alinea.adel.data as data
+from openalea.core.path import path as Path
+
 
 def adelR(nplants,dd):
     devT = devCsv('./data/axeTCa0N.csv','./data/dimTCa0N.csv','./data/phenTCa0N.csv','./data/earTCa0N.csv','./data/ssi2sen.csv')
@@ -12,16 +15,17 @@ def adelR(nplants,dd):
     pars = setAdel(devT,geoLeaf,geoAxe,nplants)
     cantable = RunAdel(dd,pars)
     return pars,cantable
-    
+
 def leaves_db(dlevel=9):
     import cPickle as Pickle
-    fn = r'../adel/data/leaves_simple.db'
+    d = data.__path__[0]
+    fn = r'%s/leaves_simple.db'%str(d)
     f = open(fn)
     leaves = Pickle.load(f)
     f.close()
     leaves,discard = fitting.fit_leaves(leaves, dlevel)
     return leaves
-       
+
 #from openalea.mtg import mtg2axialtree
 #affichage : aller voir __str__dans mtg.py
 #dp = {'plant':[1,1,1,1,1], 'axe' : [0,0,1,1,2], 'numphy': [1,2,1,2,1], 'Laz': [0,180,90,180,180],'Einc':[0,0,45,-45,45], 'El': [1,1,1,1,1],'Ev':[1,1,1,1,1], 'Esen':[0,0,0,0,0], 'Ed':[0.1,0.1,0.1,0.1,0.1]}
@@ -32,18 +36,18 @@ def leaves_db(dlevel=9):
 #more test
 p,d= adelR(1,1000)
 leaves=leaves_db()
-g=mtg_factory(d,adel_metamer,leaf_db=leaves, stand=[((0,0,0),0),((10,0,0),90), ((0,10,0), 0)])
+g=mtg_factory(d,adel_metamer,leaves=leaves, stand=[((0,0,0),0),((10,0,0),90), ((0,10,0), 0)])
 g=mtg_interpreter(g)
 scene = plot3d(g)
 pgl.Viewer.display(scene)
 #
 def test_leaf_shape():
     """ test leaf positioning/ inclination """
-    d = {'plant':[1,1],'axe_id':['MS','T1'],'ms_insertion':[0,1],'numphy':[1,1], 
+    d = {'plant':[1,1],'axe_id':['MS','T1'],'ms_insertion':[0,1],'numphy':[1,1],
          'Laz': [0,90], 'Ll' :[3,3], 'Lv' :[3,3] , 'Lsen':[0,0], 'L_shape':[3,3], 'Lw_shape':[.3,.3], 'Linc':[0,0],
          'Einc':[0,45],'El':[1,1],'Ev':[1,1],'Esen':[0,0],'Ed': [0.1,0.1]}
     g=mtg_factory(d,adel_metamer,leaf_db=leaves_db())
     g=mtg_interpreter(g)
     scene = plot3d(g)
-    pgl.Viewer.display(scene)    
+    pgl.Viewer.display(scene)
     return(g)

test/test_leaf.py

@@ -6,26 +6,33 @@
 import cPickle as Pickle
 from pylab import plot, show,clf
 
-db = r'../src/alinea/adel/data/leaves.db'
+db = r'../src/alinea/adel/data/leaves_simple.db'
 f = open(db)
 
 leaves = Pickle.load(f)
 rank = leaves.keys()[0]
 leaf = leaves[rank][0]
 f.close()
 
+dbf = r'../src/alinea/adel/data/leaves.db'
+f = open(db)
+
+leaves_f = Pickle.load(f)
+rankf = leaves.keys()[0]
+leaff = leaves[rank][0]
+f.close()
 #
 # build a database of function
 # 1. fit leaves
 # 2. write a function
 # 3. draw the result
 
-# 3 bis. write a class 
+# 3 bis. write a class
 # 4 parse the string and build the scene
-# 5. create the can file 
+# 5. create the can file
 translation = pgl.Vector3(0,0,0)
 zt = 6
-yt = 13 
+yt = 13
 
 def test1(leaf=leaf, scene = None):
     """
@@ -38,8 +45,8 @@ def test1(leaf=leaf, scene = None):
 
     x, y, s, r= leaf
     spline_leaf, leaf_surface = fitting.fit_leaf(x, y, s, r)
-    mesh = fitting.discretize(spline_leaf,30, 7, 1) 
-    
+    mesh = fitting.discretize(spline_leaf,30, 7, 1)
+
     scene += pgl.Translated(translation, mesh)
     Viewer.update()
 
@@ -65,7 +72,7 @@ def test2(leaves=leaves):
             #raw_input('Enter something for next leaf...')
         translation.y = -60 + yt*int(k)
         translation.z = 0
-            
+
 def test3(leaf=leaf, scene = None):
     """
     Obtain a leaf at different time.
@@ -79,7 +86,7 @@ def test3(leaf=leaf, scene = None):
     spline_leaf, leaf_surface = fitting.fit_leaf(x, y, s, r)
     translation = pgl.Vector3()
     n = 7
-    
+
     for i in range (1,n+1):
         mesh = fitting.partial_leaf(spline_leaf, 30, n, i, 1)
         scene += pgl.Translated(translation, mesh)
@@ -102,15 +109,15 @@ def test5(leaf=leaf):
     """
     x, y, s, r= leaf
     #spline_leaf, leaf_surface = fitting.fit_leaf(x, y, s, r)
-    tckp, u = splprep([x,y],k=5) 
+    tckp, u = splprep([x,y],k=5)
     xp, yp = splev(linspace(0,1,6),tckp)
-    #xn, yn, rn = splev(linspace(0,1,100),spline_leaf)    
+    #xn, yn, rn = splev(linspace(0,1,100),spline_leaf)
     sn=fitting.curvilinear_abscisse(x,y)
     l=sn.sum()
     clf()
     plot(x,y,'.')
     plot(xp, yp)
-    
+
 # def test6(leaves=leaves,rank=rank):
 #     # try with rank=7
 #     index = 0
@@ -130,10 +137,10 @@ def test7(leaf=leaf, scene = None):
 
     x, y, s, r= leaf
     spline_leaf, leaf_surface = fitting.fit_leaf(x, y, s, r)
-    pts, ind = fitting.mesh(spline_leaf,30, 7, 7, 1) 
+    pts, ind = fitting.mesh(spline_leaf,30, 7, 7, 1)
     fitting.write_smf('leaf_full.smf', pts, ind)
     Viewer.display(fitting.plantgl_shape(pts, ind))
-    
+
 
 def test8(leaf=leaf, scene = None):
     global translation, zt
@@ -144,7 +151,7 @@ def test8(leaf=leaf, scene = None):
     x, y, s, r= leaf
     leaf_new, leaf_surface = fitting.fit2(x, y, s, r)
 
-    pts, ind = fitting.mesh2(leaf_new, 7, 7, 1) 
+    pts, ind = fitting.mesh2(leaf_new, 7, 7, 1)
     #pts2, ind2 = fitting.qslim(13, pts, ind)
     #mesh = fitting.plantgl_shape(pts2, ind2)
 
@@ -155,7 +162,7 @@ def test8(leaf=leaf, scene = None):
     #mesh_final = mesh
     scene += pgl.Translated(translation, fitting.plantgl_shape(pts, ind))
     #scene += pgl.Translated(translation+(0,yt/3.,0), mesh_final)
-    
+
     Viewer.update()
 
 def test81(leaf=leaf, scene = None):
@@ -167,7 +174,7 @@ def test81(leaf=leaf, scene = None):
     mesh = fitting.leaf_shape2(leaf,10, 7, 7, 1)
 
     scene += pgl.Translated(translation+(0,yt/3.,0), mesh)
-    
+
     Viewer.update()
 
 # def test9(leaves=leaves):
@@ -197,10 +204,10 @@ def test81(leaf=leaf, scene = None):
 # def test10():
 #     pass
 #sc=pgl.SurfComputer(pgl.Discretizer())
-#m=pgl_shape mesh2 
+#m=pgl_shape mesh2
 #m2=pgl_shape qslim
 #m.apply(sc)
 #sc.surface
 #m2.apply(sc)
-#sc.surface 
+#sc.surface