new matrix API (#496)

* new matrix API

* suffixes

---------

Co-authored-by: pveigadecamargo <pveigadecamargo@anl.gov>

aequilibrae/distribution/gravity_calibration.py

@@ -4,6 +4,7 @@
 The procedures implemented in this code are some of those suggested in
 Modelling Transport, 4th Edition, Ortuzar and Willumsen, Wiley 2011
 """
+
 from time import perf_counter
 
 import numpy as np

aequilibrae/matrix/aequilibrae_matrix.py

@@ -5,6 +5,7 @@
 import uuid
 import warnings
 from functools import reduce
+from pathlib import Path
 from typing import List
 
 import numpy as np
@@ -90,14 +91,18 @@ def __init__(self):
         self.omx_file = None  # type: omx.File
         self.__version__ = VERSION  # Writes file version
 
-    def save(self, names=()) -> None:
+    def save(self, names=(), file_name=None) -> None:
         """Saves matrix data back to file.
 
         If working with AEM file, it flushes data to disk. If working with OMX, requires new names.
 
         :Arguments:
             **names** (:obj:`tuple(str)`, `Optional`): New names for the matrices. Required if working with OMX files
         """
+        if file_name is not None:
+            cores = names if len(names) else self.names
+            self.__save_as(file_name, cores)
+            return
 
         if not self.__omx:
             self.__flush(self.matrices)
@@ -122,6 +127,38 @@ def save(self, names=()) -> None:
         self.names = self.omx_file.list_matrices()
         self.computational_view(names)
 
+    def __save_as(self, file_name: str, cores: List[str]):
+
+        if Path(file_name).suffix.lower() == ".aem":
+            mat = AequilibraeMatrix()
+            args = {
+                "zones": self.zones,
+                "matrix_names": cores,
+                "index_names": self.index_names,
+                "memory_only": False,
+                "file_name": file_name,
+            }
+            mat.create_empty(**args)
+            mat.indices[:, :] = self.indices[:, :]
+            for core in cores:
+                mat.matrix[core][:, :] = self.matrix[core][:, :]
+            mat.name = self.name
+            mat.description = self.description
+            mat.close()
+            del mat
+
+        elif Path(file_name).suffix.lower() == ".omx":
+            omx_mat = omx.open_file(file_name, "w")
+            for core in cores:
+                omx_mat[core] = self.matrix[core]
+
+            for index in self.index_names:
+                omx_mat.create_mapping(index, self.indices[index])
+
+            omx_mat.attrs.name = self.name
+            omx_mat.attrs.description = self.description
+            omx_mat.close()
+
     def create_empty(
         self,
         file_name: str = None,
@@ -570,9 +607,9 @@ def __write__(self):
             np.memmap(self.file_path, dtype="uint8", offset=17, mode="r+", shape=1)[0] = data_size
 
             # matrix name
-            np.memmap(self.file_path, dtype="S" + str(MATRIX_NAME_MAX_LENGTH), offset=18, mode="r+", shape=1)[
-                0
-            ] = self.name
+            np.memmap(self.file_path, dtype="S" + str(MATRIX_NAME_MAX_LENGTH), offset=18, mode="r+", shape=1)[0] = (
+                self.name
+            )
 
             # matrix description
             offset = 18 + MATRIX_NAME_MAX_LENGTH
@@ -1095,9 +1132,9 @@ def setName(self, matrix_name: str):
             if len(str(matrix_name)) > MATRIX_NAME_MAX_LENGTH:
                 matrix_name = str(matrix_name)[0:MATRIX_NAME_MAX_LENGTH]
 
-            np.memmap(self.file_path, dtype="S" + str(MATRIX_NAME_MAX_LENGTH), offset=18, mode="r+", shape=1)[
-                0
-            ] = matrix_name
+            np.memmap(self.file_path, dtype="S" + str(MATRIX_NAME_MAX_LENGTH), offset=18, mode="r+", shape=1)[0] = (
+                matrix_name
+            )
 
     def setDescription(self, matrix_description: str):
         """

aequilibrae/paths/results/__init__.py

@@ -6,6 +6,7 @@
 STILL NEED TO ADD SOME EXPLANATIONS HERE
 
 """
+
 __author__ = "Pedro Camargo ($Author: Pedro Camargo $)"
 __version__ = "1.0"
 __revision__ = "$Revision: 1 $"

aequilibrae/project/network/osm_downloader.py

@@ -9,6 +9,7 @@
 
 For the original work, please see https://github.com/gboeing/osmnx
 """
+
 import logging
 import time
 import re

aequilibrae/transit/gtfs_loader.py

@@ -180,9 +180,9 @@ def __deconflict_stop_times(self) -> None:
                         )
 
                         for _, rec in max_speeds.iterrows():
-                            df.loc[
-                                (df.dist >= rec.min_distance) & ((df.dist < rec.max_distance)), "max_speed"
-                            ] = rec.speed
+                            df.loc[(df.dist >= rec.min_distance) & ((df.dist < rec.max_distance)), "max_speed"] = (
+                                rec.speed
+                            )
 
                         to_fix = df[df.max_speed < df.speed].index.values
                         if to_fix.shape[0] > 0:

aequilibrae/transit/transit_graph_builder.py

@@ -1428,9 +1428,11 @@ def to_transit_graph(self) -> TransitGraph:
         g.network["id"] = g.network.link_id
         g.prepare_graph(
             self.vertices[
-                (self.vertices.node_type == "origin")
-                if self.blocking_centroid_flows
-                else (self.vertices.node_type == "od")
+                (
+                    (self.vertices.node_type == "origin")
+                    if self.blocking_centroid_flows
+                    else (self.vertices.node_type == "od")
+                )
             ].node_id.values
         )
         g.set_graph("trav_time")

aequilibrae/utils/worker_thread.py

@@ -1,6 +1,7 @@
 """
  Original Author:  UNKNOWN. COPIED FROM STACKOVERFLOW BUT CAN'T REMEMBER EXACTLY WHERE
  """
+
 import importlib.util as iutil
 
 spec = iutil.find_spec("PyQt5")