smmregrid 0.0.1__tar.gz

smmregrid-0.0.1/LICENSE

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smmregrid-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: smmregrid
+Version: 0.0.1
+Summary: Regridding based on sparse matrix multiplication
+Author-email: Jost von Hardenberg <jost.hardenberg@polito.it>, Paolo Davini <p.davini@isac.cnr.it>, Scott Wales <scott.wales@unimelb.edu.au>
+Project-URL: Homepage, https://github.com/jhardenberg/smmregrid
+Project-URL: Bug Tracker, https://github.com/jhardenberg/smmregrid/issues
+Project-URL: Repository, https://github.com/oloapinivad/ECmean4
+Classifier: Programming Language :: Python :: 3
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Provides-Extra: tests
+Provides-Extra: all
+License-File: LICENSE
+
+[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://github.com/jhardenberg/smmregrid/graphs/commit-activity)
+[![PyTest](https://github.com/jhardenberg/smmregrid/actions/workflows/mambatest.yml/badge.svg)](https://github.com/jhardenberg/smmregrid/actions/workflows/mambatest.yml)
+[![Coverage Status](https://coveralls.io/repos/github/jhardenberg/smmregrid/badge.svg?branch=main)](https://coveralls.io/github/jhardenberg/smmregrid?branch=main)
+[![PyPI version](https://badge.fury.io/py/smmregrid.svg)](https://badge.fury.io/py/smmregrid)
+
+# smmregrid
+A compact regridder using sparse matrix multiplication
+
+This repository represents a modification of the regridding routines in [climtas](https://github.com/ScottWales/climtas) by Scott Wales, which already implements efficiently this idea and has no other significant dependencies.
+The regridder uses efficiently sparse matrix multiplication with dask + some manipulation of the coordinates. 
+
+Please note that this tool is not thought as "another interpolation tool", but rather a method to apply pre-computed weights (with CDO, which is currently tested, and with ESMF, which is not yet supported) within the python environment. 
+The speedup is estimated to be about ~1.5 to ~5 times, slightly lower if then files are written to the disk. 2D and 3D data are supported on all the grids supported by CDO, both xarray.Dataset and xarray.DataArray can be used. Masks are treated in a simple way but are correctly transfered. Attributes are kept.  
+
+The tool works for python versions >=3.8. It is safer to run it through conda/mamba. Install with: 
+
+```
+mamba env create -f environment.yml
+```
+
+then activate the environment:
+
+```
+mamba activate smmregrid
+```
+
+and install smmregrid in editable mode:
+
+```
+pip install -e .
+```
+
+Alternatively - if you have in your environment/machine the required dependencies, mostly CDO - you can install smmregrid directly via pypi with:
+
+```
+pip install smmregrid
+```
+
+Cautionary notes:
+- It does not work correctly if the Xarray.Dataset includes fields with time-varying missing points
+- It works only with interpolation methods/grids supported by CDO
+- It does not support ESMF weigths.
+

smmregrid-0.0.1/README.md

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+[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://github.com/jhardenberg/smmregrid/graphs/commit-activity)
+[![PyTest](https://github.com/jhardenberg/smmregrid/actions/workflows/mambatest.yml/badge.svg)](https://github.com/jhardenberg/smmregrid/actions/workflows/mambatest.yml)
+[![Coverage Status](https://coveralls.io/repos/github/jhardenberg/smmregrid/badge.svg?branch=main)](https://coveralls.io/github/jhardenberg/smmregrid?branch=main)
+[![PyPI version](https://badge.fury.io/py/smmregrid.svg)](https://badge.fury.io/py/smmregrid)
+
+# smmregrid
+A compact regridder using sparse matrix multiplication
+
+This repository represents a modification of the regridding routines in [climtas](https://github.com/ScottWales/climtas) by Scott Wales, which already implements efficiently this idea and has no other significant dependencies.
+The regridder uses efficiently sparse matrix multiplication with dask + some manipulation of the coordinates. 
+
+Please note that this tool is not thought as "another interpolation tool", but rather a method to apply pre-computed weights (with CDO, which is currently tested, and with ESMF, which is not yet supported) within the python environment. 
+The speedup is estimated to be about ~1.5 to ~5 times, slightly lower if then files are written to the disk. 2D and 3D data are supported on all the grids supported by CDO, both xarray.Dataset and xarray.DataArray can be used. Masks are treated in a simple way but are correctly transfered. Attributes are kept.  
+
+The tool works for python versions >=3.8. It is safer to run it through conda/mamba. Install with: 
+
+```
+mamba env create -f environment.yml
+```
+
+then activate the environment:
+
+```
+mamba activate smmregrid
+```
+
+and install smmregrid in editable mode:
+
+```
+pip install -e .
+```
+
+Alternatively - if you have in your environment/machine the required dependencies, mostly CDO - you can install smmregrid directly via pypi with:
+
+```
+pip install smmregrid
+```
+
+Cautionary notes:
+- It does not work correctly if the Xarray.Dataset includes fields with time-varying missing points
+- It works only with interpolation methods/grids supported by CDO
+- It does not support ESMF weigths.
+

smmregrid-0.0.1/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "smmregrid"
+dynamic = ["version"]
+authors = [
+  { name="Jost von Hardenberg", email="jost.hardenberg@polito.it" },
+  { name="Paolo Davini", email="p.davini@isac.cnr.it" },
+  { name="Scott Wales", email="scott.wales@unimelb.edu.au"}
+]
+description = "Regridding based on sparse matrix multiplication"
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    'numpy',
+    'xarray',
+    'dask',
+    'netcdf4',
+    'cfgrib',
+    'dask',
+    'sparse',
+    'cdo'
+]
+
+[project.optional-dependencies]
+tests = [
+    "coverage",
+    "coveralls",
+    "pytest"
+]
+
+#docs = [
+#    "sphinx",
+#    "sphinx-rtd-theme"
+#]
+
+all = [
+    "scriptengine[tests]"
+]
+
+[project.urls]
+"Homepage" = "https://github.com/jhardenberg/smmregrid"
+"Bug Tracker" = "https://github.com/jhardenberg/smmregrid/issues"
+"Repository" = "https://github.com/oloapinivad/ECmean4"
+
+[tool.setuptools.dynamic]
+version = {attr = "smmregrid.__version__"}

smmregrid-0.0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

smmregrid-0.0.1/smmregrid/__init__.py

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+"""smmregrid module"""
+
+from .regrid import Regridder, regrid
+from .cdo_weights import cdo_generate_weights
+from .util import find_vert_coord
+
+__version__ = '0.0.1'

smmregrid-0.0.1/smmregrid/cdo_weights.py

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+"""CDO-based generation of weights"""
+
+import os
+import sys
+import logging
+import tempfile
+import subprocess
+from multiprocessing import Process, Manager
+import numpy
+import xarray
+from .util import find_vert_coord
+from .weights import compute_weights_matrix3d, compute_weights_matrix, mask_weights, check_mask
+
+
+def worker(wlist, nnn, *args, **kwargs):
+    """Run a worker process"""
+    wlist[nnn] = cdo_generate_weights2d(*args, **kwargs).compute()
+
+def cdo_generate_weights(source_grid, target_grid, method="con", extrapolate=True,
+                         remap_norm="fracarea", remap_area_min=0.0, icongridpath=None,
+                         gridpath=None, extra=None, vert_coord=None, cdo="cdo", nproc=1):
+    """Generate the weights using CDO, handling both 2D and 3D cases"""
+
+    # Check if there is a vertical coordinate for 3d oceanic data
+    if not vert_coord:
+        vert_coord = find_vert_coord(source_grid)
+        logging.warning('vert_coord is %s',str(vert_coord))
+
+    if not vert_coord: # Are we 2D? Use default method
+        weights =cdo_generate_weights2d(
+            source_grid,
+            target_grid,
+            method=method,
+            extrapolate=extrapolate,
+            remap_norm=remap_norm,
+            remap_area_min=remap_area_min,
+            icongridpath=icongridpath,
+            gridpath=gridpath,
+            extra=extra,
+            cdo=cdo,
+            nproc=nproc)
+
+        # Precompute destination weights mask
+        weights_matrix = compute_weights_matrix(weights)
+        weights = mask_weights(weights, weights_matrix, vert_coord)
+        masked = int(check_mask(weights, vert_coord))
+        masked_xa = xarray.DataArray(masked, name="dst_grid_masked")
+
+        return xarray.merge([weights, masked_xa])
+
+    else:  # we are 3D
+        if extra:
+        # make sure extra is a flat list if it is not already
+            if not isinstance(extra, list):
+                extra = [extra]
+        else:
+            extra = []
+
+        if isinstance(source_grid, str):
+            sgrid = xarray.open_dataset(source_grid)
+        else:
+            sgrid = source_grid
+
+        nvert = sgrid[vert_coord].values.size
+        #print(nvert)
+
+        # for lev in range(0, nvert):
+        mgr = Manager()
+
+        # dictionaries are shared, so they have to be passed as functions
+        wlist= mgr.list(range(nvert))
+
+        num_blocks, remainder = divmod(nvert, nproc)
+        num_blocks = num_blocks + (0 if remainder == 0 else 1)
+
+        blocks = numpy.array_split(numpy.arange(nvert), num_blocks)
+        for block in blocks:
+            processes = []
+            for lev in block:
+                logging.info("Generating level: %s", str(lev))
+                extra2 = [f"-sellevidx,{lev+1}"]
+                ppp = Process(target=worker,
+                            args=(wlist, lev, source_grid, target_grid),
+                            kwargs=dict(method=method,
+                                        extrapolate=extrapolate,
+                                        remap_norm=remap_norm,
+                                        remap_area_min=remap_area_min,
+                                        icongridpath=icongridpath,
+                                        gridpath=gridpath,
+                                        extra=extra + extra2,
+                                        cdo=cdo,
+                                        nproc=nproc))
+                ppp.start()
+                processes.append(ppp)
+
+            for proc in processes:
+                proc.join()
+
+        weights = weightslist_to_3d(wlist, vert_coord)
+
+        # Precompute destination weights mask
+        weights_matrix = compute_weights_matrix3d(weights, vert_coord)
+        weights = mask_weights(weights, weights_matrix, vert_coord)
+        masked = check_mask(weights, vert_coord)
+        masked = [int(x) for x in masked]  # convert to list of int
+        masked_xa = xarray.DataArray(masked, coords={vert_coord: range(0, len(masked))}, name="dst_grid_masked")
+
+        return xarray.merge([weights, masked_xa])
+
+
+def cdo_generate_weights2d(source_grid, target_grid, method="con", extrapolate=True,
+                           remap_norm="fracarea", remap_area_min=0.0, icongridpath=None,
+                           gridpath=None, extra=None, cdo="cdo", nproc=1):
+    """
+    Generate weights for regridding using CDO
+
+    Available weight generation methods are:
+
+     * bic: SCRIP Bicubic
+     * bil: SCRIP Bilinear
+     * con: SCRIP First-order conservative
+     * con2: SCRIP Second-order conservative
+     * dis: SCRIP Distance-weighted average
+     * laf: YAC Largest area fraction
+     * ycon: YAC First-order conservative
+     * nn: Nearest neighbour
+
+    Run ``cdo gen${method} --help`` for details of each method
+
+    Args:
+        source_grid (xarray.DataArray): Source grid
+        target_grid (xarray.DataArray): Target grid
+            description
+        method (str): Regridding method - default conservative
+        extrapolate (bool): Extrapolate output field
+        remap_norm (str): Normalisation method for conservative methods
+        remap_area_min (float): Minimum destination area fraction
+        gridpath (str): where to store downloaded grids
+        icongridpath (str): location of ICON grids (e.g. /pool/data/ICON)
+        extra: command(s) to apply to source grid before weight generation (can be a list)
+        cdo: the command to launch cdo ["cdo"]
+        nproc: number of processes to use for weight generation (NOT USED!)
+
+        cdo: path to cdo binary
+    Returns:
+        :obj:`xarray.Dataset` with regridding weights
+    """
+
+    supported_methods = ["bic", "bil", "con", "con2", "dis", "laf", "nn", "ycon"]
+    if method not in supported_methods:
+        raise ValueError('The remap method provided is not supported!')
+    if remap_norm not in ["fracarea", "destarea"]:
+        raise ValueError('The remap normalization provided is not supported!')
+
+    # Make some temporary files that we'll feed to CDO
+    weight_file = tempfile.NamedTemporaryFile()
+
+    if isinstance(source_grid, str):
+        sgrid = source_grid
+    else:
+        source_grid_file = tempfile.NamedTemporaryFile()
+        source_grid.to_netcdf(source_grid_file.name)
+        sgrid = source_grid_file.name
+
+    if isinstance(target_grid, str):
+        tgrid = target_grid
+    else:
+        target_grid_file = tempfile.NamedTemporaryFile()
+        target_grid.to_netcdf(target_grid_file.name)
+        tgrid = target_grid_file.name
+
+    # Setup environment
+    env = os.environ
+    if extrapolate:
+        env["REMAP_EXTRAPOLATE"] = "on"
+    else:
+        env["REMAP_EXTRAPOLATE"] = "off"
+
+    env["CDO_REMAP_NORM"] = remap_norm
+    env["REMAP_AREA_MIN"] = "%f" % (remap_area_min)
+
+    if gridpath:
+        env["CDO_DOWNLOAD_PATH"] = gridpath
+    if icongridpath:
+        env["CDO_ICON_GRIDS"] = icongridpath
+
+    try:
+        # Run CDO
+        if extra:
+            # make sure extra is a flat list if it is not already
+            if not isinstance(extra, list):
+                extra = [extra]
+
+            subprocess.check_output(
+                [
+                    cdo,
+                    "gen%s,%s" % (method, tgrid)
+                ] + extra +
+                [
+                    sgrid,
+                    weight_file.name,
+                ],
+                stderr=subprocess.PIPE,
+                env=env,
+            )
+        else:
+            subprocess.check_output(
+                [
+                    cdo,
+                    "gen%s,%s" % (method, tgrid),
+                    sgrid,
+                    weight_file.name,
+                ],
+                stderr=subprocess.PIPE,
+                env=env,
+            )
+
+        # Grab the weights file it outputs as a xarray.Dataset
+        weights = xarray.open_dataset(weight_file.name, engine="netcdf4")
+        return weights
+
+    except subprocess.CalledProcessError as err:
+        # Print the CDO error message
+        logging.error(err.output.decode(), file=sys.stderr)
+        raise
+
+    finally:
+        # Clean up the temporary files
+        if not isinstance(source_grid, str):
+            source_grid_file.close()
+        if not isinstance(target_grid, str):
+            target_grid_file.close()
+        weight_file.close()
+
+
+def weightslist_to_3d(ds_list, vert_coord='lev'):
+    """
+    Function to combine a list of 2D cdo weights into a 3D one adding a vertical coordinate lev
+    """
+    # CDO 2.2.0 fix
+    if "numLinks" in ds_list[0].dims:
+        links_dim = "numLinks"
+    else:
+        links_dim = "num_links"
+    
+    dim_values = range(len(ds_list))
+    nl = [ds.src_address.size for ds in ds_list]
+    nl0 = max(nl)
+    nlda = xarray.DataArray(nl, coords={vert_coord: range(0, len(nl))}, name="link_length")
+    new_array = []
+    varlist = ["src_address", "dst_address", "remap_matrix", "src_grid_imask", "dst_grid_imask"]
+    ds0 = ds_list[0].drop_vars(varlist)
+    for x, d in zip(ds_list, dim_values):
+        nl1 = x.src_address.size
+#        xplist = [x[vname].pad(num_links=(0, nl0-nl1), mode='constant', constant_values=0)
+        xplist = [x[vname].pad(**{links_dim: (0, nl0-nl1), "mode": 'constant', "constant_values": 0})
+                  for vname in varlist ]
+        xp = xarray.merge(xplist)
+        new_array.append(xp.assign_coords({vert_coord: d}))
+    return xarray.merge([nlda, ds0, xarray.concat(new_array, vert_coord)])