Changes in / [ed82794:d07c883] in sasmodels

Location:

sasmodels

Files:

• compare.py (modified) (1 diff)
• core.py (modified) (1 diff)
• data.py (modified) (10 diffs)
• list_pars.py (added)

sasmodels/compare.py

@@ -604 +604 @@
 def columnize(L, indent="", width=79):
     """
-    Format a list of strings into columns for printing.
+    Format a list of strings into columns.
+
+    Returns a string with carriage returns ready for printing.
     """
     column_width = max(len(w) for w in L) + 1

sasmodels/core.py

@@ -38 +38 @@
     """
     Load a model definition given the model name.
+
+    This returns a handle to the module defining the model.  This can be
+    used with functions in generate to build the docs or extract model info.
     """
     __import__('sasmodels.models.'+model_name)

sasmodels/data.py

@@ -87 +87 @@
 
 class Data1D(object):
+    """
+    1D data object.
+
+    Note that this definition matches the attributes from sasview, with
+    some generic 1D data vectors and some SAS specific definitions.  Some
+    refactoring to allow consistent naming conventions between 1D, 2D and
+    SESANS data would be helpful.
+
+    **Attributes**
+
+    *x*, *dx*: $q$ vector and gaussian resolution
+
+    *y*, *dy*: $I(q)$ vector and measurement uncertainty
+
+    *mask*: values to include in plotting/analysis
+
+    *dxl*: slit widths for slit smeared data, with *dx* ignored
+
+    *qmin*, *qmax*: range of $q$ values in *x*
+
+    *filename*: label for the data line
+
+    *_xaxis*, *_xunit*: label and units for the *x* axis
+
+    *_yaxis*, *_yunit*: label and units for the *y* axis
+    """
     def __init__(self, x=None, y=None, dx=None, dy=None):
         self.x, self.y, self.dx, self.dy = x, y, dx, dy
@@ -93 +119 @@
         self.qmin = x.min() if x is not None else np.NaN
         self.qmax = x.max() if x is not None else np.NaN
-        self.mask = np.isnan(y) if y is not None else None
+        # TODO: why is 1D mask False and 2D mask True?
+        self.mask = (np.isnan(y) if y is not None
+                     else np.zeros_like(x,'b') if x is not None
+                     else None)
         self._xaxis, self._xunit = "x", ""
         self._yaxis, self._yunit = "y", ""
@@ -114 +143 @@
 
 class Data2D(object):
+    """
+    2D data object.
+
+    Note that this definition matches the attributes from sasview. Some
+    refactoring to allow consistent naming conventions between 1D, 2D and
+    SESANS data would be helpful.
+
+    **Attributes**
+
+    *qx_data*, *dqx_data*: $q_x$ matrix and gaussian resolution
+
+    *qy_data*, *dqy_data*: $q_y$ matrix and gaussian resolution
+
+    *data*, *err_data*: $I(q)$ matrix and measurement uncertainty
+
+    *mask*: values to exclude from plotting/analysis
+
+    *qmin*, *qmax*: range of $q$ values in *x*
+
+    *filename*: label for the data line
+
+    *_xaxis*, *_xunit*: label and units for the *x* axis
+
+    *_yaxis*, *_yunit*: label and units for the *y* axis
+
+    *_zaxis*, *_zunit*: label and units for the *y* axis
+
+    *Q_unit*, *I_unit*: units for Q and intensity
+
+    *x_bins*, *y_bins*: grid steps in *x* and *y* directions
+    """
     def __init__(self, x=None, y=None, z=None, dx=None, dy=None, dz=None):
         self.qx_data, self.dqx_data = x, dx
         self.qy_data, self.dqy_data = y, dy
         self.data, self.err_data = z, dz
-        self.mask = ~np.isnan(z) if z is not None else None
+        self.mask = (~np.isnan(z) if z is not None
+                     else np.ones_like(x) if x is not None
+                     else None)
         self.q_data = np.sqrt(x**2 + y**2)
         self.qmin = 1e-16
@@ -126 +188 @@
         self.Q_unit = "1/A"
         self.I_unit = "1/cm"
-        self.xaxis("Q_x", "A^{-1}")
-        self.yaxis("Q_y", "A^{-1}")
-        self.zaxis("Intensity", r"\text{cm}^{-1}")
+        self.xaxis("Q_x", "1/A")
+        self.yaxis("Q_y", "1/A")
+        self.zaxis("Intensity", "1/cm")
         self._xaxis, self._xunit = "x", ""
         self._yaxis, self._yunit = "y", ""
@@ -157 +219 @@
 
 class Vector(object):
+    """
+    3-space vector of *x*, *y*, *z*
+    """
     def __init__(self, x=None, y=None, z=None):
         self.x, self.y, self.z = x, y, z
@@ -235 +300 @@
     """
     Plot data loaded by the sasview loader.
+
+    *data* is a sasview data object, either 1D, 2D or SESANS.
+
+    *view* is log or linear.
+
+    *limits* sets the intensity limits on the plot; if None then the limits
+    are inferred from the data.
     """
     # Note: kind of weird using the plot result functions to plot just the
@@ -249 +321 @@
 def plot_theory(data, theory, resid=None, view='log',
                 use_data=True, limits=None):
+    """
+    Plot theory calculation.
+
+    *data* is needed to define the graph properties such as labels and
+    units, and to define the data mask.
+
+    *theory* is a matrix of the same shape as the data.
+
+    *view* is log or linear
+
+    *use_data* is True if the data should be plotted as well as the theory.
+
+    *limits* sets the intensity limits on the plot; if None then the limits
+    are inferred from the data.
+    """
     if hasattr(data, 'lam'):
         _plot_result_sesans(data, theory, resid, use_data=True, limits=limits)
@@ -258 +345 @@
 
 def protect(fn):
+    """
+    Decorator to wrap calls in an exception trapper which prints the
+    exception and continues.  Keyboard interrupts are ignored.
+    """
     def wrapper(*args, **kw):
         try:
             return fn(*args, **kw)
+        except KeyboardInterrupt:
+            raise
         except:
             traceback.print_exc()
@@ -332 +425 @@
 @protect
 def _plot_result_sesans(data, theory, resid, use_data, limits=None):
+    """
+    Plot SESANS results.
+    """
     import matplotlib.pyplot as plt
     use_data = use_data and data.y is not None
@@ -459 +555 @@
 
 def demo():
+    """
+    Load and plot a SAS dataset.
+    """
     data = load_data('DEC07086.DAT')
     set_beam_stop(data, 0.004)