Checkpoint changes from outflow forcing development

Author: akashdhruv

bin/cmd.py

@@ -23,7 +23,7 @@ class CustomCmd:
         ("with-zarr", None, "With zarr data backend"),
         ("with-dask", None, "With dask data/parallel backend"),
         ("with-server", None, "With remote server utilitiy"),
-        ("enable-testing", None, "Enable testing mode"),
+        ("enable-analysis", None, "Enable analysis mode"),
     ]
 
     def initialize_options(self):
@@ -35,7 +35,7 @@ def initialize_options(self):
         self.with_zarr = None  # pylint: disable=attribute-defined-outside-init
         self.with_dask = None  # pylint: disable=attribute-defined-outside-init
         self.with_server = None  # pylint: disable=attribute-defined-outside-init
-        self.enable_testing = None  # pylint: disable=attribute-defined-outside-init
+        self.enable_analysis = None  # pylint: disable=attribute-defined-outside-init
 
     def finalize_options(self):
         """
@@ -47,7 +47,7 @@ def finalize_options(self):
             "with_zarr",
             "with_dask",
             "with_server",
-            "enable_testing",
+            "enable_analysis",
         ]:
             if getattr(self, option) not in [None, 1]:
                 raise ValueError(f"{option} is a flag")
@@ -101,9 +101,9 @@ def run(self, user):
                 executable="/bin/bash",
             )
 
-        if self.enable_testing:
+        if self.enable_analysis:
             subprocess.run(
-                f"{sys.executable} -m pip install -r requirements/testing.txt {with_user}",
+                f"{sys.executable} -m pip install -r requirements/analysis.txt {with_user}",
                 shell=True,
                 check=True,
                 executable="/bin/bash",
@@ -116,7 +116,7 @@ def run(self, user):
             optfile.write(f"ZARR={self.with_zarr}\n")
             optfile.write(f"DASK={self.with_dask}\n")
             optfile.write(f"SERVER={self.with_server}\n")
-            optfile.write(f"TESTING={self.enable_testing}\n")
+            optfile.write(f"ANALYSIS={self.enable_analysis}\n")
 
 
 # replaces the default build command for setup.py

boxkit/__init__.py

@@ -2,8 +2,8 @@
 
 from .api import *
 from . import library
-from . import options
 from . import resources
+from . import options
 
 if options.CBOX:
     from . import cbox

boxkit/api/__init__.py

@@ -10,5 +10,5 @@
 from ._resfilter import resfilter
 from ._mean import mean_temporal
 
-if options.TESTING:
+if options.ANALYSIS:
     from ._regionprops import regionprops

boxkit/api/_create.py

@@ -29,6 +29,9 @@ def create_dataset(storage=None, **attributes):
         nxb=1,
         nyb=1,
         nzb=1,
+        xguard=0,
+        yguard=0,
+        zguard=0,
         nblockx=1,
         nblocky=1,
         nblockz=1,
@@ -46,6 +49,9 @@ def create_dataset(storage=None, **attributes):
         "nxb": int(self.nxb),
         "nyb": int(self.nyb),
         "nzb": int(self.nzb),
+        "xguard": int(self.xguard),
+        "yguard": int(self.yguard),
+        "zguard": int(self.zguard),
     }
 
     data = library.Data(storage=storage, **data_attributes)

boxkit/api/_mergeblocks.py

@@ -54,6 +54,9 @@ def mergeblocks(
         nxb=nblockx * dataset.nxb,
         nyb=nblocky * dataset.nyb,
         nzb=nblockz * dataset.nzb,
+        xguard=0 if dataset.nxb == 1 else 1,
+        yguard=0 if dataset.nyb == 1 else 1,
+        zguard=0 if dataset.nzb == 1 else 1,
         xmin=dataset.xmin,
         ymin=dataset.ymin,
         zmin=dataset.zmin,
@@ -113,7 +116,17 @@ def map_blk_to_merged_dset(blk_sorted, merged_dataset, varlist):
     for varkey in varlist:
         for block in merged_dataset.blocklist:
             block[varkey][
-                blk_sorted.nzb * kloc : blk_sorted.nzb * (kloc + 1),
-                blk_sorted.nyb * jloc : blk_sorted.nyb * (jloc + 1),
-                blk_sorted.nxb * iloc : blk_sorted.nxb * (iloc + 1),
-            ] = blk_sorted[varkey][:, :, :]
+                blk_sorted.nzb * kloc
+                + block.zguard : blk_sorted.nzb * (kloc + 1)
+                + block.zguard,
+                blk_sorted.nyb * jloc
+                + block.yguard : blk_sorted.nyb * (jloc + 1)
+                + block.yguard,
+                blk_sorted.nxb * iloc
+                + block.xguard : blk_sorted.nxb * (iloc + 1)
+                + block.xguard,
+            ] = blk_sorted[varkey][
+                blk_sorted.zguard : blk_sorted.nzb + blk_sorted.zguard,
+                blk_sorted.yguard : blk_sorted.nyb + blk_sorted.yguard,
+                blk_sorted.xguard : blk_sorted.nxb + blk_sorted.xguard,
+            ]

boxkit/api/_read.py

@@ -46,12 +46,14 @@ def read_dataset(
 
     """
     if not source:
-        source = "test-sample"
+        source = "sample"
 
     if not storage:
         storage = "numpy-memmap"
 
-    data_attributes, block_attributes = resources.read.options[source](
+    source = getattr(resources, source)
+
+    data_attributes, block_attributes = source.read(
         filename, server, nthreads, batch, monitor, backend
     )
 

boxkit/api/_regionprops.py

@@ -22,6 +22,10 @@ def regionprops(dataset, lsetkey, backend="serial", nthreads=1, monitor=False):
     labelkey = "bwlabel"
     dataset.addvar(labelkey, dtype=int)
 
+    normals = ["normx", "normy"]
+    for norm in normals:
+        dataset.addvar(norm)
+
     region = api.create_region(dataset)
 
     skimage_props_blk.nthreads = nthreads
@@ -34,6 +38,8 @@ def regionprops(dataset, lsetkey, backend="serial", nthreads=1, monitor=False):
     listprops = list(itertools.chain.from_iterable(listprops))
 
     dataset.delvar(labelkey)
+    for norm in normals:
+        dataset.delvar(norm)
 
     return listprops
 
@@ -66,7 +72,14 @@ def skimage_props_blk(block, lsetkey, labelkey):
             corners.append([block.zmin, block.ymin, block.xmin][idim])
 
     listprops = skimage_measure.regionprops(
-        numpy.reshape(block[labelkey], shape).astype(int)
+        numpy.reshape(
+            block[labelkey][
+                block.zguard : block.nzb + block.zguard,
+                block.yguard : block.nyb + block.yguard,
+                block.xguard : block.nxb + block.xguard,
+            ],
+            shape,
+        ).astype(int)
     )
     ndim = len(shape)
 

boxkit/library/_block.py

@@ -82,7 +82,9 @@ def xrange(self, location):
             "node": self.__class__.get_node_loc,
         }
 
-        return range_dict[location](self.xmin, self.xmax, self.dx, self.nxb)
+        return range_dict[location](
+            self.xmin, self.xmax, self.dx, self.nxb, self.xguard
+        )
 
     def yrange(self, location):
         """
@@ -93,7 +95,9 @@ def yrange(self, location):
             "node": self.__class__.get_node_loc,
         }
 
-        return range_dict[location](self.ymin, self.ymax, self.dy, self.nyb)
+        return range_dict[location](
+            self.ymin, self.ymax, self.dy, self.nyb, self.yguard
+        )
 
     def zrange(self, location):
         """
@@ -104,19 +108,29 @@ def zrange(self, location):
             "node": self.__class__.get_node_loc,
         }
 
-        return range_dict[location](self.zmin, self.zmax, self.dz, self.nzb)
+        return range_dict[location](
+            self.zmin, self.zmax, self.dz, self.nzb, self.zguard
+        )
 
     @staticmethod
-    def get_center_loc(min_val, max_val, delta, num_points):
+    def get_center_loc(min_val, max_val, delta, num_points, num_guards):
         """Private method for center location"""
-        return numpy.linspace(min_val + delta / 2, max_val - delta / 2, num_points)
+        return numpy.linspace(
+            min_val + delta / 2 - num_guards * delta,
+            max_val - delta / 2 + num_guards * delta,
+            num_points + 2 * num_guards,
+        )
 
     @staticmethod
     def get_node_loc(
-        min_val, max_val, delta, num_points
+        min_val, max_val, delta, num_points, num_guards
     ):  # pylint: disable=unused-argument
         """Private method for face location"""
-        return numpy.linspace(min_val, max_val, num_points)
+        return numpy.linspace(
+            min_val - num_guards * delta,
+            max_val + num_guards * delta,
+            num_points + 2 * num_guards,
+        )
 
     def _set_attributes(self, attributes):
         """

boxkit/library/_dataset.py

@@ -215,6 +215,39 @@ def halo_exchange(  # pylint: disable=too-many-arguments
         for varkey in varlist:
             halo_exchange_block((block for block in self.blocklist), varkey)
 
+    def fill_guard_cells(self, varlist):
+        """
+        Fill guard cells
+        """
+        # Convert single string to a list
+        if isinstance(varlist, str):
+            varlist = [varlist]
+
+        if len(self.blocklist) > 1:
+            raise NotImplementedError(
+                "[boxkit.library.create.Dataset] fill_guard_cells is only implemented for blocklist == 1"
+            )
+
+        for block in self.blocklist:
+            for var in varlist:
+                for bnd in range(block.xguard):
+                    block[var][:, :, bnd] = block[var][:, :, block.xguard]
+                    block[var][:, :, bnd + block.nxb + block.xguard] = block[var][
+                        :, :, block.nxb + block.xguard - 1
+                    ]
+
+                for bnd in range(block.yguard):
+                    block[var][:, bnd, :] = block[var][:, block.yguard, :]
+                    block[var][:, bnd + block.nyb + block.yguard, :] = block[var][
+                        :, block.nyb + block.yguard - 1, :
+                    ]
+
+                for bnd in range(block.zguard):
+                    block[var][bnd, :, :] = block[var][block.zguard, :, :]
+                    block[var][bnd + block.nzb + block.zguard, :, :] = block[var][
+                        block.nzb + block.zguard - 1, :, :
+                    ]
+
 
 @Action
 def halo_exchange_block(block, varkey):

boxkit/options.py

@@ -3,4 +3,4 @@
 ZARR=None
 DASK=None
 SERVER=None
-TESTING=1
+ANALYSIS=1

boxkit/resources/__init__.py

@@ -1,2 +1,4 @@
 """Initialize resources"""
-from . import read
+
+from . import sample
+from . import flash

boxkit/resources/flash/__init__.py

@@ -0,0 +1,11 @@
+"""Initializate flash module"""
+
+from ._read import read
+from ... import options
+
+if options.ANALYSIS == 1:
+    from ._lset import (
+        bubble_contour_plot,
+        bubble_normal_vectors,
+        bubble_shape_measurement,
+    )