Merge branch 'master' of github.com:DamCB/tyssue

tests/core/test_generation.py

@@ -102,3 +102,25 @@ def test_anchors():
 
     res_srce_trgt_anchors = sheet.edge_df.loc[18:, ['srce', 'trgt']]
     assert res_srce_trgt_anchors.equals(expected_res)
+
+
+def test_sheet_extract():
+    datasets, specs = generation.three_faces_sheet()
+    sheet = Sheet('test_sheet_extract_coordinate', datasets, specs)
+    subsheet = sheet.sheet_extract('is_alive')
+    assert subsheet.face_df['is_alive'].all() == True
+
+
+def test_sheet_extract_coordinate():
+    grid = hexa_grid2d(6, 4, 3, 3)
+    datasets = from_2d_voronoi(Voronoi(grid))
+    sheet = Sheet('test_extract_bounding_box', datasets)
+    subsheet = sheet.extract_bounding_box(
+                        [sheet.face_df['x'].min(), sheet.face_df['x'].max()/2],
+                        [sheet.face_df['y'].min(), sheet.face_df['y'].max()/2])
+    assert subsheet.face_df['x'].max() <= sheet.face_df['x'].max()/2
+    assert subsheet.face_df['x'].min() >= sheet.face_df['x'].min()
+    assert subsheet.face_df['y'].max() <= sheet.face_df['y'].max()/2
+    assert subsheet.face_df['y'].min() >= sheet.face_df['y'].min()
+    assert subsheet.face_df['z'].max() <= sheet.face_df['z'].max()
+    assert subsheet.face_df['z'].min() >= sheet.face_df['z'].min()

tyssue/behaviors/sheet_events.py

@@ -74,7 +74,7 @@ def ab_pull(self, face, *args):
         verts = self.sheet.edge_df[self.sheet.edge_df['face'] ==
                                    self.idx_lookup(face)]['srce'].unique()
         factor = args[0]
-        new_tension = self.sheet.specs['edge']['line_tension'] * factor
+        new_tension = self.sheet.specs['edge']['radial_tension'] * factor
         self.sheet.vert_df.loc[verts, 'radial_tension'] += new_tension
 
     def divide(self, face, *args):

tyssue/core/sheet.py

@@ -78,8 +78,8 @@ def get_neighborhood(self, face, order):
         # Start with the face so that it's not gathered later
         neighbors = pd.DataFrame.from_dict({'face': [face],
                                             'order': [0]})
-        for k in range(order+1):
-            for neigh in neighbors[neighbors['order'] == k-1]['face']:
+        for k in range(order + 1):
+            for neigh in neighbors[neighbors['order'] == k - 1]['face']:
                 new_neighs = self.get_neighbors(neigh)
                 new_neighs = set(new_neighs).difference(neighbors['face'])
 
@@ -91,6 +91,85 @@ def get_neighborhood(self, face, order):
 
         return neighbors.reset_index(drop=True).loc[1:]
 
+    def sheet_extract(self, face_mask, coords=['x', 'y', 'z']):
+        """ Extract a new sheet from the embryo sheet
+        that correspond to a key word that define a face.
+        Parameters
+        ----------
+        sheet: a :class:Sheet object
+        face_mask : column name in face composed by boolean value
+        coords
+        Returns
+        -------
+        sheet_fold_patch_extract :
+            subsheet corresponding to the fold patch area.
+
+        """
+        x, y, z = coords
+        datasets = {}
+
+        datasets['face'] = self.face_df[
+            self.face_df[face_mask] == True].copy()
+        datasets['edge'] = self.edge_df[self.edge_df['face'].isin(
+            datasets['face'].index)].copy()
+        datasets['vert'] = self.vert_df.loc[self.edge_df['srce'].unique()]
+
+        subsheet = Sheet('subsheet', datasets, self.specs)
+        subsheet.reset_index()
+        subsheet.reset_topo()
+        return (subsheet)
+
+    def extract_bounding_box(self, x_boundary=None, y_boundary=None,
+                             z_boundary=None, coords=['x', 'y', 'z']):
+        """ Extract a new sheet from the embryo sheet
+        that correspond to boundary coordinate
+        define by the user.
+        Parameters
+        ----------
+        sheet: a :class:Sheet object
+        xmin, xmax : boundary
+        ymin, ymax : boundary
+        zmin, zmax : boundary
+        coords
+
+        Returns
+        -------
+        sheet_extract :
+            subsheet
+
+        """
+        x, y, z = coords
+        datasets = {}
+        datasets['face'] = self.face_df.copy()
+
+        if x_boundary is not None:
+            xmin, xmax = x_boundary
+            datasets['face'] = datasets['face'][
+                (datasets['face']['x'] > xmin) & (datasets['face']['x'] < xmax)
+            ].copy()
+
+        if y_boundary is not None:
+            ymin, ymax = y_boundary
+            datasets['face'] = datasets['face'][
+                (datasets['face']['y'] > ymin) & (datasets['face']['y'] < ymax)
+            ].copy()
+
+        if z_boundary is not None:
+            zmin, zmax = z_boundary
+            datasets['face'] = datasets['face'][
+                (datasets['face']['z'] > zmin) & (datasets['face']['z'] < zmax)
+            ].copy()
+
+        datasets['edge'] = self.edge_df[self.edge_df['face'].isin(
+            datasets['face'].index)].copy()
+
+        datasets['vert'] = self.vert_df.loc[self.edge_df['srce'].unique()]
+
+        subsheet = Sheet('subsheet', datasets, self.specs)
+        subsheet.reset_index()
+        subsheet.reset_topo()
+        return (subsheet)
+
     @classmethod
     def planar_sheet_2d(cls, identifier,
                         nx, ny, distx, disty):