Merge 8c168c6 into acbcf0a

.gitignore

@@ -84,6 +84,7 @@ celerybeat-schedule
 .env
 
 # virtualenv
+Pipfile
 .venv
 venv/
 venv3/

src/cr/cube/cube.py

@@ -268,6 +268,22 @@ def inflate(self):
             self._mask_size,
         )
 
+    @lazyproperty
+    def is_mr_by_itself(self):
+        """It identify if the cube contains MRxItself as last 2 dimensions.
+
+        If the last 2 dimensions in cube (ndim>=3) are MR and they have
+        the same alias returns True
+        """
+        return (
+            # ---there are at least three dimensions---
+            self.ndim >= 3
+            # ---the last two are both MR---
+            and all(dim_type == DT.MR for dim_type in self.dimension_types[-2:])
+            # ---and they both have the same alias---
+            and len(set([dimension.alias for dimension in self.dimensions[-2:]])) == 1
+        )
+
     @lazyproperty
     def is_weighted(self):
         """True if cube response contains weighted data."""

src/cr/cube/cubepart.py

@@ -57,9 +57,8 @@ def factory(
         return _Slice(cube, slice_idx, transforms, population, mask_size)
 
     @lazyproperty
-    def variable_name(self):
-        """str representing the name of the superheading variable."""
-        return self._dimensions[0 if self.ndim < 2 else 1].name
+    def cube_is_mr_by_itself(self):
+        return False
 
     @lazyproperty
     def dimension_types(self):
@@ -97,6 +96,11 @@ def shape(self):
             "must be implemented by each subclass"
         )  # pragma: no cover
 
+    @lazyproperty
+    def variable_name(self):
+        """str representing the name of the superheading variable."""
+        return self._dimensions[0 if self.ndim < 2 else 1].name
+
 
 class _Slice(CubePartition):
     """2D cube partition.
@@ -167,6 +171,10 @@ def columns_margin(self):
     def counts(self):
         return np.array([row.values for row in self._matrix.rows])
 
+    @lazyproperty
+    def cube_is_mr_by_itself(self):
+        return self._cube.is_mr_by_itself
+
     @lazyproperty
     def description(self):
         """str description of this slice, which it takes from its rows-dimension."""
@@ -182,6 +190,35 @@ def inserted_column_idxs(self):
     def inserted_row_idxs(self):
         return tuple(i for i, row in enumerate(self._matrix.rows) if row.is_insertion)
 
+    @lazyproperty
+    def insertions(self):
+        """Returns masked array with residuals for insertions
+
+                 0     1	 2	     3	    4	    5	    6
+           0   inf   inf   inf	   inf	  inf	 -2.9	  inf
+           1   inf	 inf   inf	   inf	  inf	 -4.3	  inf
+           2   2.5	 1.3   3.3	 -0.70	-7.25	 -6.52	 2.25
+           3   inf	 inf   inf	   inf	  inf	 -2.51	  inf
+           4  -1.16	 2.20  5.84	  1.78	-8.48	 -5.92	 0.93
+           5   inf   inf   inf	   inf	  inf	  9.70	  inf
+
+           Only the insertions residuals are showed in a inf masked array
+        """
+        inserted_rows = self.inserted_row_idxs
+        inserted_cols = self.inserted_column_idxs
+        if not inserted_cols and not inserted_cols:
+            return []
+        mask = np.zeros(self.pvals.shape)
+        mask[inserted_rows, :] = 1
+        mask[:, inserted_cols] = 1
+        masked_pvals = np.ma.masked_array(self.pvals, np.logical_not(mask)).filled(
+            np.inf
+        )
+        masked_zscores = np.ma.masked_array(self.zscore, np.logical_not(mask)).filled(
+            np.inf
+        )
+        return np.stack([masked_pvals, masked_zscores])
+
     @lazyproperty
     def is_empty(self):
         return any(s == 0 for s in self.shape)
@@ -202,6 +239,10 @@ def name(self):
         """
         return self.rows_dimension_name
 
+    @lazyproperty
+    def overlaps_tstats(self):
+        return self._matrix.overlaps_tstats
+
     @lazyproperty
     def pairwise_indices(self):
         alpha = self._transforms_dict.get("pairwise_indices", {}).get("alpha", 0.05)
@@ -245,6 +286,14 @@ def population_counts(self):
     def pvals(self):
         return np.array([row.pvals for row in self._matrix.rows])
 
+    @lazyproperty
+    def residual_test_stats(self):
+        """Exposes pvals and zscore (with HS) stacked together
+
+        Public method used as cube_method for the SOA API
+        """
+        return np.stack([self.pvals, self.zscore])
+
     @lazyproperty
     def row_base(self):
         return np.array([row.base for row in self._matrix.rows])
@@ -458,6 +507,10 @@ def table_name(self):
 
         title = self._cube.name
         table_name = self._cube.dimensions[0].valid_elements[self._slice_idx].label
+
+        if self._cube.is_mr_by_itself:
+            return title
+
         return "%s: %s" % (title, table_name)
 
     @lazyproperty

src/cr/cube/dimension.py

@@ -258,6 +258,15 @@ def __init__(self, dimension_dict, dimension_type, dimension_transforms=None):
         self._dimension_type = dimension_type
         self._dimension_transforms_arg = dimension_transforms
 
+    @lazyproperty
+    def alias(self):
+        """Return the alias for the dimension if it exists, None otherwise
+
+        This property is needed to identify one of the mandatory condition
+        for a MRxItself cube.
+        """
+        return self._dimension_dict["references"].get("alias", None)
+
     @lazyproperty
     def all_elements(self):
         """_AllElements object providing cats or subvars of this dimension.