Merge pull request #25 from amoodie/refactor

Refactor

README.md

@@ -1,8 +1,7 @@
 # rivers2stratigraphy
 
 
-Explore how a river becomes stratigraphy.
-
+Explore how a river becomes stratigraphy
 
 <img src="https://github.com/amoodie/rivers2stratigraphy/blob/master/private/rivers2stratigraphy_demo.gif" alt="demo_gif">
 
@@ -13,6 +12,13 @@ This repository is also linked into the [SedEdu suite of education modules](http
 
 
 
+## About the model
+Stratigraphic model based on LAB models, i.e., geometric channel body is deposited in "matrix" of floodplain mud. 
+The channel is always fixed to the basin surface and subsidence is only control on vertical stratigraphy.
+Horizontal stratigraphy is set by 1) lateral migration (drawn from a pdf) and dampened for realism, and 2) avulsion that is set to a fixed value.
+
+
+
 ## Installation and running the module
 
 Visit the section of the text below for more information on installing and executing the `rivers2stratigraphy` program on your computer. 
@@ -73,16 +79,17 @@ Finally, run the module from the Python shell with:
 import rivers2stratigraphy
 ```
 
-You will be asked if you wish to launch the module now, type `Y` and hit enter.
+Instructions will indicate to use the following command to then run the module:
+```
+rivers2stratigraphy.run()
+```
 
 
-Alternatively, run the module with provided script:
+Alternatively, run the module with provided script (this is the hook used for launching from SedEdu):
 ```
 python3 <path-to-installation>/run_rivers2stratigraphy.py
 ```
 
-Note that this may throw an error on closing the window, but this is not a problem to functionality.
-
 
 Please [open an issue](https://github.com/amoodie/rivers2stratigraphy/issues) if you encounter any additional error messages! 
 Please include 1) operating system, 2) installation method, and 3) copy-paste the error.
@@ -96,6 +103,7 @@ If you are interested in contributing to code please see below for instructions.
 
 If you are interested in contributing to the the accompanying activites (which would be greatly appreciated!) please see [Writing Activites for SedEdu](https://github.com/amoodie/sededu/blob/develop/docs/writing_activities.md)
 
+
 #### Download the source code
 
 You can download this entire repository as a `.zip` by clicking the "Clone or download button on this page", or by [clicking here](https://github.com/amoodie/rivers2stratigraphy/archive/master.zip) to get a `.zip` folder. Unzip the folder in your preferred location.

about.json

@@ -1,7 +1,7 @@
 {
     "title": "Rivers to Stratigraphy",
     "author": "Andrew J. Moodie",
-    "version": "0.2.0",
+    "version": "0.2.6",
     "shortdesc": "Explore how a migrating river becomes stratigraphy",
     "difficulty": 7,
     "license": "MIT",

rivers2stratigraphy/__init__.py

@@ -1,3 +1,8 @@
-from . import launcher
+print('\n\n    SedEdu -- rivers2stratigraphy module')
 
-launcher.import_runner()
+print('\n\nTo run the activity use command:\n')
+print('rivers2stratigraphy.run()\n')
+
+def run():
+    from . import gui
+    gui.Runner()

rivers2stratigraphy/_version.py

@@ -1 +1 @@
-__version__ = "0.2.5"
+__version__ = "0.2.6"

rivers2stratigraphy/channel.py

@@ -1,7 +1,6 @@
 
 import numpy as np
 from matplotlib.patches import Polygon, Rectangle
-from matplotlib.collections import PatchCollection, LineCollection
 import shapely.geometry as sg
 import shapely.ops as so
 

rivers2stratigraphy/gui.py

@@ -0,0 +1,137 @@
+"""
+rivers2stratigraphy GUI -- build river stratigraphy interactively
+  Stratigraphic model based on LAB models, i.e., geometric channel body is  
+  deposited in "matrix" of floodplain mud. The channel is always fixed to the 
+  basin surface and subsidence is only control on vertical stratigraphy.
+  Horizontal stratigraphy is set by 1) lateral migration (drawn from a pdf) 
+  and dampened for realism, and 2) avulsion that is set to a fixed value.
+  
+  written by Andrew J. Moodie
+  amoodie@rice.edu
+  Feb 2018
+
+"""
+
+
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.animation as animation
+
+from .strat import Strat
+from .slider_manager import SliderManager
+from .channel import ActiveChannel, State, ChannelBody
+from . import geom, sedtrans, utils
+
+
+class GUI(object):
+
+    """     
+    main GUI object that selects parameters for initialization and
+    handles creation of all the needed parts of the model. This class is
+    initialized below by class Runner if this file is run as __main__ 
+    """
+
+    def __init__(self):
+        # initial conditions
+
+        config = utils.Config()
+
+        # model run params
+        config.dt = 100 # timestep in yrs
+        self._paused = False
+
+        # setup params
+        config.Cf = 0.004 # friction coeff
+        config.D50 = 300*1e-6
+        config.Beta = 1.5 # exponent to avulsion function
+        config.Df = 0.6 # dampening factor to lateral migration rate change
+        config.dxdtstd = 1 # stdev of lateral migration dist, [m/yr]?
+
+        # constants
+        config.conR = 1.65
+        config.cong = 9.81
+        config.conrhof = 1000
+        config.connu = 1.004e-6
+        config.Rep = geom.Repfun(config.D50, config.conR, config.cong, config.connu) # particle Reynolds num
+
+        # water discharge slider params
+        config.Qw = config.Qwinit = 1000
+        config.Qwmin = 200
+        config.Qwmax = 4000
+        config.Qwstep = 100
+
+        # subsidence slider params
+        config.sig = config.siginit = 2
+        config.sigmin = 0
+        config.sigmax = 5
+        config.sigstep = 0.2
+
+        # avulsion timescale slider params
+        config.Ta = config.Tainit = 500
+        config.Tamin = config.dt
+        config.Tamax = 1500
+        config.Tastep = 10
+
+        # yView slider params
+        config.yView = config.yViewinit = 100
+        config.yViewmin = 25
+        config.yViewmax = 250
+        config.yViewstep = 25
+
+        # basin width slider params
+        config.Bb = config.Bbinit = 4000 # width of belt (m)
+        config.Bbmin = 1
+        config.Bbmax = 10
+        config.Bbstep = 0.5
+
+        # additional initializations
+        config.Bast = 0 # Basin top level
+
+        # setup the figure
+        plt.rcParams['toolbar'] = 'None'
+        plt.rcParams['figure.figsize'] = 8, 6
+        self.fig, self.strat_ax = plt.subplots()
+        self.fig.canvas.set_window_title('SedEdu -- rivers2stratigraphy')
+        plt.subplots_adjust(left=0.085, bottom=0.1, top=0.95, right=0.5)
+        self.strat_ax.set_xlabel("channel belt (km)")
+        self.strat_ax.set_ylabel("stratigraphy (m)")
+        plt.ylim(-config.yView, 0.1*config.yView)
+        plt.xlim(-config.Bb/2, config.Bb/2)
+        self.strat_ax.xaxis.set_major_formatter( plt.FuncFormatter(
+                            lambda v, x: str(v / 1000).format('%0.0f')) )
+
+        # add sliders
+        self.config = config
+        self.sm = SliderManager(self)
+
+
+    def pause_anim(self, event):
+        """
+        pause animation by altering hidden var
+        """
+        if self._paused:
+            self._paused = False
+        else:
+            self._paused = True
+
+
+
+class Runner(object):
+    def __init__(self):
+        gui = GUI()
+
+        # time looping
+        gui.strat = Strat(gui)
+
+        anim = animation.FuncAnimation(gui.fig, gui.strat, 
+                                       interval=100, blit=False,
+                                       save_count=None)
+
+        plt.show()
+
+
+
+if __name__ == '__main__':
+    runner = Runner()
+
+