Merge pull request #165 from RangamaniLabUCSD/emmetfrancis/latex-tables

Fixes to Latex table formatting

examples/example3/example3_withaxisymm.ipynb

@@ -425,7 +425,7 @@
     "        \"final_t\": 1,\n",
     "        \"initial_dt\": 0.01,\n",
     "        \"time_precision\": 6,\n",
-    "        \"attempt_timestep_restart_on_divergence\": True\n",
+    "        # \"attempt_timestep_restart_on_divergence\": True\n",
     "    }\n",
     ")\n",
     "config_cur.flags.update({\"axisymmetric_model\": True})"
@@ -627,7 +627,7 @@
     "            \"final_t\": 1,\n",
     "            \"initial_dt\": 0.01,\n",
     "            \"time_precision\": 6,\n",
-    "            \"attempt_timestep_restart_on_divergence\": True,\n",
+    "            # \"attempt_timestep_restart_on_divergence\": True,\n",
     "        }\n",
     "    )\n",
     "    config_cur.flags.update({\"axisymmetric_model\": True})\n",

smart/mesh_tools.py

@@ -1438,16 +1438,19 @@ def load_mesh(
     if extra_keys is None:
         extra_keys = []
 
-    if not pathlib.Path(filename).is_file():
+    if isinstance(filename, str):
+        filename = pathlib.Path(filename)
+
+    if not filename.is_file():
         raise FileNotFoundError(f"File {filename} does not exists")
 
     if mesh is None:
         mesh = d.Mesh(comm)
 
-        with d.HDF5File(comm, pathlib.Path(filename).with_suffix(".h5").as_posix(), "r") as hdf5:
+        with d.HDF5File(comm, filename.with_suffix(".h5").as_posix(), "r") as hdf5:
             hdf5.read(mesh, "/mesh", False)
 
-    dim = mesh.geometric_dimension()
+    dim = mesh.topology().dim()  # geometric_dimension()
     mf_cell = d.MeshFunction("size_t", mesh, dim)
     mf_facet = d.MeshFunction("size_t", mesh, dim - 1)
     subdomains = []

smart/model.py

@@ -474,6 +474,12 @@ def _init_2_1_reactions_to_symbolic_strings(self):
                 raise ValueError(
                     "Reaction %s does not seem to have an associated equation" % reaction.name
                 )
+            if reaction.eqn_f_str == "":
+                reaction.eqn_str = f"-{reaction.eqn_r_str}"
+            elif reaction.eqn_r_str == "":
+                reaction.eqn_str = f"{reaction.eqn_f_str}"
+            else:
+                reaction.eqn_str = f"{reaction.eqn_f_str}-{reaction.eqn_r_str}"
 
     def _init_2_2_check_reaction_validity(self):
         """Confirms that all reactions have parameters/species defined"""
@@ -986,7 +992,11 @@ def _init_4_7_set_initial_conditions(self):
                     # restrict to specified subdomain
                     u_cur = self.cc[species.compartment_name].u[ukey]
                     u_new = create_restriction(u_cur, species.subdomain_data, species.subdomain_val)
-                    u_cur.assign(u_new)
+                    values = u_cur.vector().get_local()
+                    values_new = u_new.vector().get_local()
+                    values[species.dof_map] = values_new[species.dof_map]
+                    u_cur.vector().set_local(values)
+                    u_cur.vector().apply("insert")
 
     def _init_5_1_reactions_to_fluxes(self):
         """Convert reactions to flux objects"""

smart/model_assembly.py

@@ -219,8 +219,8 @@ def print_to_latex(
         self,
         properties_to_print=None,
         max_col_width=None,
-        sig_figs=2,
-        return_df=True,
+        sig_figs=3,
+        return_df=False,
     ):
         """
         Print object properties in latex format.
@@ -242,7 +242,33 @@ def print_to_latex(
 
         for row in range(df.shape[0]):
             for col in range(df.shape[1]):
-                if isinstance(df.iat[row, col], str):
+                if df.columns[col] == "eqn_str":
+                    cur_str = df.iat[row, col]
+                    cur_str = "$" + cur_str + "$"
+                    cur_str = cur_str.replace("**", "^")
+                    idx = 0
+                    while idx < len(cur_str):
+                        if cur_str[idx] == "_":
+                            cur_str = cur_str[0 : idx + 1] + "{" + cur_str[idx + 1 :]
+                            isMath = False
+                            testIdx = idx + 2
+                            while not isMath:
+                                if not (cur_str[testIdx].isalnum() or cur_str[testIdx] == "_"):
+                                    if cur_str[testIdx] == "*":
+                                        cur_str = cur_str[0:testIdx] + "} " + cur_str[testIdx + 1 :]
+                                    else:
+                                        cur_str = cur_str[0:testIdx] + "}" + cur_str[testIdx:]
+                                    isMath = True
+                                else:
+                                    testIdx += 1
+                            idx = testIdx + 2
+                        elif cur_str[idx] == "*":
+                            cur_str = cur_str[0:idx] + " " + cur_str[idx + 1 :]
+                            idx += 1
+                        else:
+                            idx += 1
+                    df.iloc[row, col] = cur_str
+                elif isinstance(df.iat[row, col], str):
                     cur_str = df.iat[row, col]
                     if "_" in cur_str:
                         df.iloc[row, col] = cur_str.replace("_", "\_")
@@ -259,23 +285,23 @@ def print_to_latex(
                                 new_list[i] = "`"
                     cur_str = "".join(new_list)
                     df.iloc[row, col] = cur_str
-        for col in df.columns:
-            # Convert quantity objects to unit
-            if isinstance(df[col].iloc[0], pint.Quantity):
-                # if tablefmt=='latex':
-                df[col] = df[col].apply(lambda x: f"${x:0.{sig_figs}e~Lx}$")
-
-            if col == "idx":
-                df = df.drop("idx", axis=1)
+                # Convert quantity objects to unit
+                elif isinstance(df.iat[row, col], pint.Quantity):
+                    x = df.iat[row, col]
+                    if isinstance(x.magnitude, str):
+                        df.iloc[row, col] = f"{x:s~P}"
+                    else:
+                        df.iloc[row, col] = f"${x:0.{sig_figs}e~Lx}$"
 
+        for col in df.columns:
             if "_" in col:
                 df = df.rename(columns={col: col.replace("_", "\_")})
 
         if return_df:
             return df
         else:
             with pandas.option_context("max_colwidth", 1000):
-                logger.info(df.to_latex(escape=False, longtable=True, index=False))
+                logger.info(df.to_latex(escape=False, longtable=True, index=True))
 
     def get_pandas_dataframe_formatted(
         self,
@@ -326,11 +352,14 @@ def print(
         )
 
         # # Change certain df entries to best format for printing
-        for col in df.columns:
-            # Convert quantity objects to unit
-            if isinstance(df[col].iloc[0], pint.Quantity):
-                # if tablefmt=='latex':
-                df[col] = df[col].apply(lambda x: f"{x:0.{sig_figs}e~P}")
+        for row in range(df.shape[0]):
+            for col in range(df.shape[1]):
+                if isinstance(df.iat[row, col], pint.Quantity):
+                    x = df.iat[row, col]
+                    if isinstance(x.magnitude, str):
+                        df.iloc[row, col] = f"{x:s~P}"
+                    else:
+                        df.iloc[row, col] = f"{x:0.{sig_figs}e~P}"
 
         # print to file
         if filename is None:
@@ -447,7 +476,7 @@ def __init__(self):
 
         self.properties_to_print = [
             "_quantity",
-            "is_time_dependent",
+            # "is_time_dependent",
             "sym_expr",
             "notes",
             "group",
@@ -760,8 +789,7 @@ def __init__(self):
         self.properties_to_print = [
             "compartment_name",
             "_Diffusion",
-            "initial_condition",
-            "concentration_units",
+            "_Initial_Concentration",
         ]
 
     def print(
@@ -774,33 +802,9 @@ def print(
         for s in self:
             s.D_quantity
             s.latex_name
+            s.initial_condition_quantity
         super().print(tablefmt, self.properties_to_print, filename, max_col_width)
 
-    def print_to_latex(
-        self,
-        properties_to_print=None,
-        max_col_width=None,
-        sig_figs=2,
-        return_df=False,
-    ):
-        properties_to_print = ["_latex_name"]
-        properties_to_print.extend(self.properties_to_print)
-        df = super().print_to_latex(properties_to_print, max_col_width, sig_figs, return_df=True)
-        # fix dof_index
-        for col in df.columns:
-            if col == "dof_index":
-                df[col] = df[col].astype(int)
-        # fix name
-        # get the column of df that contains the name
-        # this can be more robust
-        # df.columns
-
-        if return_df:
-            return df
-        else:
-            with pandas.option_context("max_colwidth", 1000):
-                logger.info(df.to_latex(escape=False, longtable=True, index=False))
-
 
 @dataclass
 class Species(ObjectInstance):
@@ -841,7 +845,6 @@ class Species(ObjectInstance):
     def to_dict(self):
         "Convert to a dict that can be used to recreate the object."
         keys_to_keep = [
-            "name",
             "initial_condition",
             "concentration_units",
             "D",
@@ -1139,7 +1142,7 @@ class ReactionContainer(ObjectContainer):
     def __init__(self):
         super().__init__(Reaction)
 
-        self.properties_to_print = ["lhs", "rhs", "eqn_f_str", "eqn_r_str"]
+        self.properties_to_print = ["lhs", "rhs", "eqn_str", "topology"]
 
     def print(
         self,
@@ -1217,6 +1220,8 @@ class Reaction(ObjectInstance):
     track_value: bool = False
     eqn_f_str: str = ""
     eqn_r_str: str = ""
+    eqn_str: str = ""
+    topology: str = ""
     group: str = ""
     axisymm: bool = False
     has_subdomain: bool = False
@@ -1235,6 +1240,7 @@ def to_dict(self):
             "track_value",
             "eqn_f_str",
             "eqn_r_str",
+            "eqn_str",
             "group",
             "axisymm",
         ]