Merge pull request #14 from spectraphilic/figure-cache

Introduce a cache for figures that removes the need of the explicit FIG param

.travis.yml

@@ -48,6 +48,11 @@ python:
   - 2.7
   - 3.5
 
+before_script:
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
+  - sleep 3 # give xvfb some time to start
+
 script:
   - py.test reflexible -v --cov reflexible --cov-report term-missing
   # reflexible is far from being PEP8 compatible yet, but in the future maybe wise to use the line below...

reflexible/__init__.py

@@ -99,11 +99,13 @@ def print_versions():
                                      "uio_examples/HelloWorld_V9.02/outputs"),
 }
 
+
 # Import the public functions here
 from .tests.all import test
 from . import conv2netcdf4
 from .scripts.create_ncfile import create_ncfile
 from .data_structures import (Header, Command, Release,
                               ReleasePoint, Ageclass)
+from .utils import Structure, CacheDict
 
 from .base_read import read_trajectories

reflexible/data_structures.py

@@ -374,7 +374,7 @@ def __init__(self, path=None, nested=False, absolute_path=True):
         self.nested = nested
         self.absolute_path = absolute_path
 
-        # check for nested or not, assumes only two nc files in 
+        # check for nested or not, assumes only two nc files in
         # output directory
         if nested:
             ncfile = [d for d in files if 'nest' in d][0]
@@ -513,10 +513,12 @@ def __getitem__(self, item):
             d = FD.grid_dates[pointspec]
             c = FD[(nspec, d)]
             c.slabs = get_slabs(self.Heightnn, c.data_cube)
+            c.total_column = np.squeeze(np.sum(c.data_cube, axis=2))
+            c.foot_print = c.data_cube[:,:,0]
 
         return c
 
-
+# TODO: Following John, the get_slabs function should be deprecated
 def get_slabs(Heightnn, grid):
     """Preps grid for plotting.
 
@@ -659,7 +661,7 @@ def min(self):
 
 
 class Command(object):
-    """ General COMMAND input for Flexpart 
+    """ General COMMAND input for Flexpart
 
     #TODO: use properties ??
     """
@@ -707,10 +709,10 @@ def __init__(self, **options):
             'MDOMAINFILL': [0,
                             '''If MDOMAINFILL is set to 1, the first box specified in file   RELEASES is used as the domain where domain-filling trajectory calculations are to be done. Particles are initialized uniformly distributed (according to the air mass distribution) in that domain at the beginning of the simulation, and are created at the boundaries throughout the simulation perio'''],
             'IND_SOURCE': [1, '''IND_SOURCE switches between different units for concentrations at  the source NOTE that in backward simulations the release of computational particles takes place at   the "receptor" and the sampling of particles at the "source".
-                1=mass units (for bwd-runs = concentration)   
+                1=mass units (for bwd-runs = concentration)
                 2=mass mixing ratio units'''],
             'IND_RECEPTOR': [1, '''IND_RECEPTOR switches between different units for concentrations at the receptor
-                          1=mas s units (concentrations) 
+                          1=mas s units (concentrations)
                           2=mas s mixing ratio units'''],
             'MQUASILAG': [0,
                           '''MQUASILAG indicates whether particles shall be numbered consecutively (1) or with their release location number (0). The first option allows tracking of individual particles using the partposit output files'''],
@@ -809,7 +811,7 @@ def to_file(self, cfile):
 
 
 class Ageclass(object):
-    """ General COMMAND input for Flexpart 
+    """ General COMMAND input for Flexpart
 
     """
 

reflexible/mapping.py

@@ -20,6 +20,8 @@
 import matplotlib.pyplot as plt
 from mpl_toolkits import basemap
 
+from reflexible import Structure
+
 # mpl.use("Agg")
 # mp.interactive(False)
 # mpl.use('Agg')
@@ -28,20 +30,6 @@
 __version__ = "0.03"
 
 
-class Structure(dict):
-
-    def __getattr__(self, attr):
-        return self[attr]
-
-    def __setattr__(self, attr, value):
-        self[attr] = value
-
-    def set_with_dict(self, D):
-        """ set attributes with a dict """
-        for k in D.keys():
-            self.__setattr__(k, D[k])
-
-
 def map_regions(map_region='default', map_par=None, fig_par=None):
     """Given a `map_region`, return the associated parameters in mapping DB.
 
@@ -243,99 +231,6 @@ def draw_grid(m, xdiv=10., ydiv=5., location=[1, 0, 0, 1],
     return m_p, m_m
 
 
-def get_FIGURE(fig=None, ax=None, m=None, map_region=None,
-               getm=True, map_par=None, fig_par=None,
-               image=None):
-    """
-    This is a core function, used throughout this module. It is called
-    by various functions. The idea is that I create a :class:`Structure` that
-    contains the figure, ax, and m instance. I also add a field for "indices".
-    I'm not sure this all makes the most sense, but it is what I came up with
-    in order to be able to reuse figures. This saves a huge amount of time, as
-    creating then basemap instance can be time consuming.
-    This whole concept overall really needs to be reviewed!
-
-    .. note::
-        Generally you won't use this function direction.
-
-    USAGE::
-
-        > FIG = get_FIGURE()
-        or
-        > FIG = get_FIGURE(map_region='polarcat')
-
-    Returns
-       This will return the "FIG" object, which has attributes: `fig`, `ax`,
-       `m`, and `indices`. The indices are used for deleting lines, texts,
-       collections, etc. if and when we are reusing the figure instance. The
-       indices basically give us a reference to the *empty* map, so we can
-       delete lines without losing meridians or parallels for example.
-
-
-    ============      ======================================
-    keys              description
-    ============      ======================================
-    fig               a pyplot.fig instance, use
-                      plt.figure(FIG.fig.number) to make the
-                      fig active (for example to use
-                      plt.savefig('filename.png')
-    m                 The basemap instance so you can do:
-                      x,y = FIG.m(lon,lat)
-    ax                The axes
-    indices           with index for texts, images, lines,
-                      and collections
-    ============      ======================================
-
-
-
-    """
-    FIGURE = Structure()
-
-    if getm:
-        if m is None:
-            if image:
-                fig, m = get_base_image(image, map_region=map_region,
-                                        map_par=map_par,
-                                        fig_par=fig_par,
-                                        )
-            else:
-
-                fig, m = get_base1(map_region=map_region,
-                                   map_par=map_par,
-                                   fig_par=fig_par,
-                                   fig=fig,
-                                   )
-
-            FIGURE.fig = fig
-            FIGURE.m = m
-            FIGURE.ax = fig.gca()
-    elif m is None:
-        FIGURE.m = None
-    else:
-        FIGURE.m = m
-
-    if fig is None:
-        FIGURE.fig = plt.figure()
-        fig = FIGURE.fig
-    else:
-        FIGURE.fig = fig
-
-    if ax is None:
-        FIGURE.ax = fig.gca()
-        ax = FIGURE.ax
-    else:
-        FIGURE.ax = ax
-
-    FIGURE.indices = Structure()
-    FIGURE.indices.texts = len(FIGURE.ax.texts)
-    FIGURE.indices.images = len(FIGURE.ax.images)
-    FIGURE.indices.collections = len(FIGURE.ax.collections)
-    FIGURE.indices.lines = len(FIGURE.ax.lines)
-
-    print("Using figure: %s" % FIGURE.fig.number)
-    return FIGURE
-
-
 def get_base1(map_region=1,
               figname=None,
               fig=None,