Updating README

Still need to add some explanations in the Tutorials section

Author: eleanorcamp

README.rst

@@ -14,12 +14,13 @@ Table of Contents
 -----------------
 
 - `Installation <#installation>`__
+- `Tutorials <#tutorials>`__
 - `Usage <#usage>`__
 - `Features <#features>`__
-- `Gallery <#gallery>`__
+- `Contributing <#contributing>`__
+- `License <#license>`__
 - `Contact <#contact>`__
-- `Support <#support>`__
-- `Citations <#citations>`__
+- `Acknowledgments <#acknowledgments>`__
 
 Documentation
 -------------
@@ -66,27 +67,120 @@ To install TreeSim_Lpy, follow these steps (adapted from the `L-Py documentation
 
       lpy
 
-6. **Install TreeSim_Lpy**:
 
-   With the conda environment for L-Py set, next we need to clone the TreeSim_Lpy repository. To do that run
+Tutorials
+---------
 
-   .. code-block:: sh
+There are many things you may want to modify as you grow your own trees. Here are some tutorials for some of the more common changes:
+
+1. **Changing Apple Geometry:**
+   
+   The call production of the apples happens in the ``grow_object(o)`` section:
+
+   .. code-block:: python
+
+       elif 'Apple' in o.name:
+           produce [S(.1/2, .09/15)f(.1)&(180)A(.1, .09)]
+   
+   
+
+   The apple's base is generated with the ``A(bh, r)`` production rule seen below. 
+
+   .. code-block:: python
+      
+      A(bh, r):
+          curves = make_apple_curve()
+          base_curve = curves[0]
+          top_curve = curves[1]
+          nproduce SetColor(230,0,0) SectionResolution(60)
+          produce nF(bh, .01, r, base_curve) ^(180) nF(bh/5, .1, r, top_curve)^(180)#S(bh/2,r/15)
+   
+   The parameters represent the base height of the apple and the radius of the apple. If you wanted to create a completely new apple geometry, just replace the code in this A section. However, if you simply want to edit the existing shape of the apple, that can be done in the ``make_apple_curve()`` section. 
+
+   The apple is made with two curves: a curve that marks the base of the apple, and a curve that marks the indentation on top of the apple. These curves are generated as different Curve2D objects, then turned into QuantisedFunction objects. This is necessary because of the way the apple is produced ``nF``. ``nF`` has an optional parameter ``radiusvariation`` which must be a quantized function. ``nF`` produces a cylinder in n steps, and these curves work by specifying how large the radius for the cylinder should be at each step.
+   
+   Currently, the stem is produced separately from the apple base. The stem is created in a slightly different way than the apple. A NurbsCurve2D object is returned from the ``make_stem_curve()`` function. This curve is used in ``SetGuide`` to mark how the stem will be generated. ``nF`` is used to follow the guide while generating a cylinder, and there is no ``radiusvariation`` this time.
+
+   .. code-block:: python
+
+       S(sh,r):
+           stem_curve = make_stem_curve()
+           nproduce SetColor(100,65,23) 
+           produce  SetGuide(stem_curve, sh) _(r)nF(sh, .1, r)
+
+
+2. **Changing Leaf Geometry:**
+
+   .. code-block:: python
+
+      L(l):
+          nproduce SetColor(0,225,0) 
+  
+          curves = make_leaf_guide()
+          curve1 = curves[0]
+          curve2 = curves[1]
+  
+          produce _(.0025) F(l/10){[SetGuide(curve1, l) _(.001).nF(l, .01)][SetGuide(curve2, l)_(.001).nF(l, .01)]}
 
-      git clone https://github.com/OSUrobotics/treesim_lpy.git
 
-Usage
------
+3. **Changing Bud Geometry:**
+   
+   .. code-block:: python
 
-Here is a basic usage example to get you started:
+      spiked_bud(r):
+          base_height = r * 2
+          top_height = r * 2
+          num_sect = 20
+          produce @g(Cylinder(r,base_height,1,num_sect))f(base_height)@g(Cone(r,top_height,0,num_sect))
 
-- **Loading a Tree Model:**
+4. **Changing Branch Profile Curve:**
 
    .. code-block:: python
 
-      Do some lpy things
-      More lpy code
-      produce something?
+      # From grow_object(o)
+      if 'Trunk' in o.name or 'Branch' in o.name:
+        nproduce SetContour(o.contour)
+      else:
+        # set the contour back to a usual circle
+        reset_contour()
+
+5. **Changing Tertiary Branch Curves:**
+
+   .. code-block:: python
 
+      # From bud(t)
+      if 'NonTrunk' in new_object.name:
+         import time
+         curve = create_bezier_curve(seed_val=time.time())
+         nproduce [SetGuide(curve, new_object.max_length)
+
+6. **Changing color ID system:**
+
+   .. code-block:: python
+
+      # From grow_object(o)
+      r, g, b = o.color
+      nproduce SetColor(r, g, b)
+      
+      smallest_color = [r, g, b].index(min([r, g, b]))
+      o.color[smallest_color] += 1
+
+7. **Changing Apple and Leaf ratio:**
+   
+   .. code-block:: python
+
+      # From Spur class
+      def create_branch(self):
+          if self.num_leaves < self.max_leaves: 
+              self.num_leaves += 1
+              if rd.random()<0.9:
+                  new_ob = Leaf(copy_from = self.prototype_dict['leaf'])
+              else:
+                  new_ob = Apple(copy_from = self.prototype_dict['apple'])
+          else: 
+              new_ob = None
+          
+          return new_ob
 
 
 Features
@@ -101,7 +195,7 @@ Gallery
 ========
 .. figure:: media/envy_model.png
    :width: 500
-   :height: 300
+   :height: 500
    
    Example of a labelled, pruned and tied envy tree system using TreeSim_Lpy
   
@@ -120,7 +214,7 @@ Contact
 For any questions or issues, please contact us through **GitHub Issues**. 
 
 
-Support
+Help and Support
 ----------------
 
 Please open an **Issue** if you need support or you run into any error (Installation, Runtime, etc.).