From 401b42b9ab4ce7fcbafffb2ea0b0f35673fd54f1 Mon Sep 17 00:00:00 2001 From: fraserwg Date: Tue, 23 Nov 2021 15:00:18 +0000 Subject: [PATCH] updated the tests to deal with tiled datasets --- xmitgcm/test/test_mds_store.py | 219 ++++++++++++++++---------- xmitgcm/test/test_utils.py | 280 ++++++++++++++++++++++++++------- 2 files changed, 356 insertions(+), 143 deletions(-) diff --git a/xmitgcm/test/test_mds_store.py b/xmitgcm/test/test_mds_store.py index b8c38023..89b98162 100644 --- a/xmitgcm/test/test_mds_store.py +++ b/xmitgcm/test/test_mds_store.py @@ -18,7 +18,10 @@ # a meta test def test_file_hiding(all_mds_datadirs): dirname, _ = all_mds_datadirs - basenames = ['XC.data', 'XC.meta'] + if _['tiled']: + basenames = ['XC.001.001.data', 'XC.001.001.meta'] + else: + basenames = ['XC.data', 'XC.meta'] for basename in basenames: assert os.path.exists(os.path.join(dirname, basename)) with hide_file(dirname, *basenames): @@ -39,7 +42,7 @@ def test_open_mdsdataset_minimal(all_mds_datadirs): ds = xmitgcm.open_mdsdataset( dirname, iters=None, read_grid=False, swap_dims=False, - geometry=expected['geometry']) + geometry=expected['geometry'], tiled=expected['tiled']) # the expected dimensions of the dataset eshape = expected['shape'] @@ -98,7 +101,7 @@ def test_read_grid(all_mds_datadirs): dirname, expected = all_mds_datadirs ds = xmitgcm.open_mdsdataset( dirname, iters=None, read_grid=True, - geometry=expected['geometry']) + geometry=expected['geometry'], tiled=expected['tiled']) for vname in _EXPECTED_GRID_VARS: assert vname in ds.variables @@ -121,12 +124,12 @@ def test_values_and_endianness(all_mds_datadirs): # default endianness ds = xmitgcm.open_mdsdataset( dirname, iters=None, read_grid=True, swap_dims=False, - geometry=expected['geometry']) + geometry=expected['geometry'], tiled=expected['tiled']) # now reverse endianness ds_le = xmitgcm.open_mdsdataset( dirname, iters=None, read_grid=True, endian='<', swap_dims=False, - geometry=expected['geometry']) + geometry=expected['geometry'], tiled=expected['tiled']) for vname, (idx, val) in expected['expected_values'].items(): np.testing.assert_allclose(ds[vname].values[idx], val) @@ -140,73 +143,84 @@ def test_open_dataset_no_meta(all_mds_datadirs): """Make sure we read variables with no .meta files.""" dirname, expected = all_mds_datadirs - shape = expected['shape'] - - nz = shape[0] - ny, nx = shape[-2:] - shape_2d = shape[1:] - dims_2d = ('j', 'i') - if expected['geometry'] == 'llc': - dims_2d = ('face',) + dims_2d - ny = nx*shape[-3] - elif expected['geometry'] == 'cs': - dims_2d = ('j', 'face', 'i') - if len(shape) == 4: - nz, ny, nface, nx = shape - elif len(shape) == 3: - ny, nface, nx = shape - - dims_3d = dims_2d if nz == 1 else ('k',) + dims_2d - dims_2d = ('time',) + dims_2d - dims_3d = ('time',) + dims_3d - it = expected['test_iternum'] - kwargs = dict(iters=it, geometry=expected['geometry'], read_grid=False, - swap_dims=False, default_dtype=expected['dtype']) - # a 3D file - to_hide = ['T.%010d.meta' % it, 'Eta.%010d.meta' % it] - with hide_file(dirname, *to_hide): - ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], **kwargs) - print(ds['T'].dims) - print(dims_3d) - assert ds['T'].dims == dims_3d - assert ds['T'].values.ndim == len(dims_3d) - assert ds['Eta'].dims == dims_2d - assert ds['Eta'].values.ndim == len(dims_2d) - - with pytest.raises(IOError): - xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], iters=it, - geometry=expected['geometry'], - read_grid=False) - pytest.fail("Expecting IOError when default_dtype " - "is not precised (i.e., None)") - - # now get rid of the variables used to infer dimensions - with hide_file(dirname, 'XC.meta', 'RC.meta'): - with pytest.raises(IOError): + if expected['tiled']: + meta_files = glob(dirname + '/*.meta') + to_hide = [os.path.split(meta_file)[1] for meta_file in meta_files] + with hide_file(dirname, *to_hide): + # Do not yet support opening tiled files without metadata. Test we get an error. + with pytest.raises(IOError): + xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], iters=it, + geometry=expected['geometry'], + read_grid=False, tiled=expected['tiled']) + else: + shape = expected['shape'] + + nz = shape[0] + ny, nx = shape[-2:] + shape_2d = shape[1:] + dims_2d = ('j', 'i') + if expected['geometry'] == 'llc': + dims_2d = ('face',) + dims_2d + ny = nx*shape[-3] + elif expected['geometry'] == 'cs': + dims_2d = ('j', 'face', 'i') + if len(shape) == 4: + nz, ny, nface, nx = shape + elif len(shape) == 3: + ny, nface, nx = shape + + dims_3d = dims_2d if nz == 1 else ('k',) + dims_2d + dims_2d = ('time',) + dims_2d + dims_3d = ('time',) + dims_3d + + + kwargs = dict(iters=it, geometry=expected['geometry'], read_grid=False, + swap_dims=False, default_dtype=expected['dtype'], tiled=expected['tiled']) + + to_hide = ['T.%010d.meta' % it, 'Eta.%010d.meta' % it] + with hide_file(dirname, *to_hide): ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], **kwargs) - if expected['geometry']=='llc': - ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], - nx=nx, nz=nz, **kwargs) - with hide_file(dirname, *to_hide): + print(ds['T'].dims) + print(dims_3d) + assert ds['T'].dims == dims_3d + assert ds['T'].values.ndim == len(dims_3d) + assert ds['Eta'].dims == dims_2d + assert ds['Eta'].values.ndim == len(dims_2d) + + with pytest.raises(IOError): + xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], iters=it, + geometry=expected['geometry'], + read_grid=False) + pytest.fail("Expecting IOError when default_dtype " + "is not precised (i.e., None)") + + # now get rid of the variables used to infer dimensions + with hide_file(dirname, 'XC.meta', 'RC.meta'): + with pytest.raises(IOError): + ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], **kwargs) + if expected['geometry']=='llc': ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], - nx=nx, nz=nz, **kwargs) - else: - ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], - nx=nx, ny=ny, nz=nz, **kwargs) - with hide_file(dirname, *to_hide): + nx=nx, nz=nz, **kwargs) + with hide_file(dirname, *to_hide): + ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], + nx=nx, nz=nz, **kwargs) + else: ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], - nx=nx, ny=ny, nz=nz, **kwargs) - - # try just hiding RC - with hide_file(dirname, 'RC.meta'): - if expected['geometry']=='llc': - ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], - nz=nz, **kwargs) - else: - ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], - nz=nz, **kwargs) + nx=nx, ny=ny, nz=nz, **kwargs) + with hide_file(dirname, *to_hide): + ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], + nx=nx, ny=ny, nz=nz, **kwargs) + + # try just hiding RC + with hide_file(dirname, 'RC.meta'): + if expected['geometry']=='llc': + ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], + nz=nz, **kwargs) + else: + ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'], + nz=nz, **kwargs) def test_open_dataset_2D_diags(all_mds_datadirs): # convert 3D fields with only 2D diagnostic output @@ -228,31 +242,54 @@ def test_open_dataset_2D_diags(all_mds_datadirs): it = expected['test_iternum'] kwargs = dict(iters=it, geometry=expected['geometry'], read_grid=False, - swap_dims=False) - - to_hide = ['T.%010d.meta' % it, 'T.%010d.data' % it] + swap_dims=False, tiled=expected['tiled']) + + if expected['tiled']: + N_tilex = int(nx / expected['len_tilex']) + N_tiley = int(ny / expected['len_tiley']) + + to_hide = [] + for n_tilex in range(1, N_tilex + 1): + for n_tiley in range(1, N_tiley + 1): + to_hide += ['T.{:010d}.{:03d}.{:03d}.data'.format( + it, n_tilex, n_tiley)] + to_hide += ['T.{:010d}.{:03d}.{:03d}.meta'.format( + it, n_tilex, n_tiley)] + else: + to_hide = ['T.%010d' % it + '.data', 'T.%010d' % it + '.meta'] + with hide_file(dirname, *to_hide): ldir = py.path.local(dirname) - old_prefix = 'Eta.%010d' % it - new_prefix = 'T.%010d' % it - for suffix in ['.data', '.meta']: - lp = ldir.join(old_prefix + suffix) - lp.copy(ldir.join(new_prefix + suffix)) - + if expected['tiled']: + for n_tilex in range(1, N_tilex + 1): + for n_tiley in range(1, N_tiley + 1): + suffix = '.{:03d}.{:03d}'.format(n_tilex, n_tiley) + old_prefix = 'Eta.%010d' % it + suffix + new_prefix = 'T.%010d' % it + suffix + for extension in ['.data', '.meta']: + lp = ldir.join(old_prefix + extension) + lp.copy(ldir.join(new_prefix + extension)) + else: + old_prefix = 'Eta.%010d' % it + new_prefix = 'T.%010d' % it + for extension in ['.data', '.meta']: + lp = ldir.join(old_prefix + extension) + lp.copy(ldir.join(new_prefix + extension)) + ds = xmitgcm.open_mdsdataset(dirname, prefix=['T'], **kwargs) def test_swap_dims(all_mds_datadirs): """See if we can swap dimensions.""" dirname, expected = all_mds_datadirs - kwargs = dict(iters=None, read_grid=True, geometry=expected['geometry']) + kwargs = dict(iters=None, read_grid=True, geometry=expected['geometry'], tiled=expected['tiled']) expected_dims = ['XC', 'XG', 'YC', 'YG', 'Z', 'Zl', 'Zp1', 'Zu'] # make sure we never swap if not reading grid assert 'i' in xmitgcm.open_mdsdataset(dirname, - iters=None, read_grid=False, geometry=expected['geometry']) + iters=None, read_grid=False, geometry=expected['geometry'], tiled=expected['tiled']) if expected['geometry'] in ('llc', 'cs', 'curvilinear'): # make sure swapping is not the default ds = xmitgcm.open_mdsdataset(dirname, **kwargs) @@ -267,7 +304,7 @@ def test_swap_dims(all_mds_datadirs): ds = xmitgcm.open_mdsdataset( dirname, geometry=expected['geometry'], iters=None, read_grid=True, swap_dims=True, - grid_vars_to_coords=True) + grid_vars_to_coords=True, tiled=expected['tiled']) # check for comodo metadata needed by xgcm @@ -291,9 +328,9 @@ def test_swap_dims(all_mds_datadirs): assert set(ds.dims.keys()) == set(expected_dims) # make sure swapping works with multiple iters - ds = xmitgcm.open_mdsdataset(dirname, geometry=expected['geometry'], + ds = xmitgcm.open_mdsdataset(dirname, geometry=expected['geometry'], tiled=expected['tiled'], prefix=['S']) - #print(ds) + ds.load() assert 'XC' in ds['S'].dims assert 'YC' in ds['S'].dims @@ -308,7 +345,7 @@ def test_prefixes(all_mds_datadirs): iters = [expected['test_iternum']] ds = xmitgcm.open_mdsdataset( dirname, iters=iters, prefix=prefixes, - read_grid=False, geometry=expected['geometry']) + read_grid=False, geometry=expected['geometry'], tiled=expected['tiled']) for p in prefixes: assert p in ds @@ -319,12 +356,19 @@ def test_separate_grid_dir(all_mds_datadirs): dirname, expected = all_mds_datadirs prefixes = ['U', 'V', 'W', 'T', 'S', 'PH'] # , 'PHL', 'Eta'] iters = [expected['test_iternum']] + + if expected['tiled']: + XC_meta_file = 'XC.001.001.meta' + XC_data_file = 'XC.001.001.data' + else: + XC_meta_file = 'XC.meta' + XC_data_file = 'XC.data' with hide_file(dirname, - *['XC.meta', 'XC.data', 'RC.meta', 'RC.data']) as grid_dir: + *[XC_meta_file, XC_data_file, 'RC.meta', 'RC.data']) as grid_dir: ds = xmitgcm.open_mdsdataset( dirname, grid_dir=grid_dir, iters=iters, prefix=prefixes, - read_grid=False, geometry=expected['geometry']) + read_grid=False, geometry=expected['geometry'], tiled=expected['tiled']) for p in prefixes: assert p in ds @@ -336,7 +380,8 @@ def test_multiple_iters(multidim_mds_datadirs): ds = xmitgcm.open_mdsdataset( dirname, read_grid=False, geometry=expected['geometry'], iters=expected['all_iters'], - prefix=expected['prefixes']) + prefix=expected['prefixes'], + tiled=expected['tiled']) assert list(ds.iter.values) == expected['all_iters'] # now infer the iters, should be the same @@ -512,7 +557,7 @@ def test_drc_length(all_mds_datadirs): os.path.join(dirname, 'DRC.meta')) ds = xmitgcm.open_mdsdataset( dirname, iters=None, read_grid=True, - geometry=expected['geometry']) + geometry=expected['geometry'], tiled=expected['tiled']) assert len(ds.drC) == (len(ds.drF)+1) @@ -565,7 +610,7 @@ def test_mask_values(all_mds_datadirs): dirname, expected = all_mds_datadirs ds = xmitgcm.open_mdsdataset( dirname, iters=None, read_grid=True, - geometry=expected['geometry']) + geometry=expected['geometry'], tiled=expected['tiled']) hFac_list = ['hFacC', 'hFacW', 'hFacS'] mask_list = ['maskC', 'maskW', 'maskS'] diff --git a/xmitgcm/test/test_utils.py b/xmitgcm/test/test_utils.py index 84a2cb2c..0ccf1c41 100644 --- a/xmitgcm/test/test_utils.py +++ b/xmitgcm/test/test_utils.py @@ -1,3 +1,4 @@ +from mmap import mmap import pytest import os import numpy as np @@ -6,7 +7,7 @@ from xmitgcm.test.test_xmitgcm_common import (hide_file, file_md5_checksum, all_mds_datadirs, mds_datadirs_with_diagnostics, llc_mds_datadirs, layers_mds_datadirs, all_grid_datadirs, mds_datadirs_with_inputfiles, - _experiments, cs_mds_datadirs) + _experiments, cs_mds_datadirs, tiled_mds_datadirs, untiled_mds_datadirs) from xmitgcm.file_utils import listdir @@ -20,6 +21,10 @@ nrecords = [ 1 ]; """ +def test_tiled_test(tiled_mds_datadirs): + assert True + + def test_parse_meta(tmpdir): """Check the parsing of MITgcm .meta into python dictionary.""" @@ -120,7 +125,10 @@ def test_read_raw_data(tmpdir, dtype): # a meta test of our own utitity funcion def test_file_hiding(all_mds_datadirs): dirname, _ = all_mds_datadirs - basenames = ['XC.data', 'XC.meta'] + if _['tiled']: + basenames = ['XC.001.001.data', 'XC.001.001.meta'] + else: + basenames = ['XC.data', 'XC.meta'] listed_files = listdir(dirname) for basename in basenames: assert os.path.exists(os.path.join(dirname, basename)) @@ -134,10 +142,10 @@ def test_file_hiding(all_mds_datadirs): assert os.path.exists(os.path.join(dirname, basename)) -def test_read_mds(all_mds_datadirs): +def test_read_mds(untiled_mds_datadirs): """Check that we can read mds data from .meta / .data pairs""" - dirname, expected = all_mds_datadirs + dirname, expected = untiled_mds_datadirs from xmitgcm.utils import read_mds @@ -195,8 +203,8 @@ def test_read_mds(all_mds_datadirs): assert isinstance(res[prefix], np.ndarray) # make sure endianness works - res = read_mds(basename, use_dask=False, use_mmap=False) - testval = res[prefix].newbyteorder('<')[0, 0] + res = read_mds(basename, use_dask=False, use_mmap=False, endian='>') + testval = res[prefix].newbyteorder('S')[0, 0] res_endian = read_mds(basename, use_mmap=False, endian='<', use_dask=False) val_endian = res_endian[prefix][0, 0] @@ -251,6 +259,70 @@ def test_read_mds(all_mds_datadirs): use_mmap=False, extra_metadata=emeta) +def test_read_tiled_mds(tiled_mds_datadirs): + """Check that we can read mds data from .meta / .data pairs""" + + dirname, expected = tiled_mds_datadirs + + from xmitgcm.utils import read_tiled_mds + + prefix = 'XC' + basename = os.path.join(dirname, prefix) + # should be dask by default + res = read_tiled_mds(basename) + assert isinstance(res, dict) + assert prefix in res + assert isinstance(res[prefix], dask.array.core.Array) + + # try some options + with pytest.raises(NotImplementedError): + res = read_tiled_mds(basename, use_dask=False) + + res = read_tiled_mds(basename, use_dask=False, use_mmap=False) + assert isinstance(res, dict) + assert prefix in res + assert isinstance(res[prefix], np.ndarray) + + with pytest.raises(NotImplementedError): + res = read_tiled_mds(basename, chunks="2D") + + # test the extra_metadata + if expected['geometry'] == 'llc': + emeta = {'has_faces': True, 'ny': 13*90, 'nx': 90, + 'ny_facets': [3*90, 3*90, 90, 3*90, 3*90], + 'face_facets': [0, 0, 0, 1, 1, 1, 2, 3, 3, 3, 4, 4, 4], + 'facet_orders': ['C', 'C', 'C', 'F', 'F'], + 'face_offsets': [0, 1, 2, 0, 1, 2, 0, 0, 1, 2, 0, 1, 2], + 'transpose_face': [False, False, False, + False, False, False, False, + True, True, True, True, True, True]} + else: + emeta = None + + # make sure endianness works + res = read_tiled_mds(basename, use_dask=False, use_mmap=False, endian='>') + testval = res[prefix].newbyteorder('S')[0, 0] + res_endian = read_tiled_mds(basename, use_mmap=False, + endian='<', use_dask=False) + val_endian = res_endian[prefix][0, 0] + np.testing.assert_allclose(testval, val_endian) + + # try reading with iteration number + prefix = 'T' + basename = os.path.join(dirname, prefix) + iternum = expected['test_iternum'] + res = read_tiled_mds(basename, iternum=iternum) + assert prefix in res + assert isinstance(res[prefix], dask.array.core.Array) + + res = read_tiled_mds(basename, iternum=iternum, use_dask=False, + use_mmap=False) + assert isinstance(res, dict) + assert prefix in res + assert isinstance(res[prefix], np.ndarray) + + + def test_read_mds_tokens(mds_datadirs_with_diagnostics): from xmitgcm.utils import read_mds dirname, expected = mds_datadirs_with_diagnostics @@ -270,8 +342,12 @@ def test_read_mds_tokens(mds_datadirs_with_diagnostics): def test_read_mds_no_meta(all_mds_datadirs): - from xmitgcm.utils import read_mds dirname, expected = all_mds_datadirs + if expected['tiled']: + from xmitgcm.utils import read_tiled_mds as read_mds + else: + from xmitgcm.utils import read_mds + shape = expected['shape'] ny, nx = shape[-2:] if len(shape) == 4: @@ -285,7 +361,10 @@ def test_read_mds_no_meta(all_mds_datadirs): shape_2d = (ny, nx) shape_3d = shape_2d if nz == 1 else (nz,) + shape_2d - prefixes = {'XC': shape_2d, 'hFacC': shape_3d} + if expected['tiled']: + prefixes = {'XC.001.001': shape_2d, 'hFacC.001.001': shape_3d} + else: + prefixes = {'XC': shape_2d, 'hFacC': shape_3d} for prefix, shape in prefixes.items(): basename = os.path.join(dirname, prefix) @@ -293,19 +372,25 @@ def test_read_mds_no_meta(all_mds_datadirs): # can't read without specifying shape and dtype with pytest.raises(IOError): res = read_mds(basename) - res = read_mds(basename, shape=shape, dtype=dtype, legacy=True) - assert isinstance(res, dict) - assert prefix in res - # should be dask by default - assert isinstance(res[prefix], dask.array.core.Array) - assert res[prefix].shape == shape + + if expected['tiled']: + with pytest.raises(IOError): + res = read_mds(basename, shape=shape, + dtype=dtype, legacy=True) + else: + res = read_mds(basename, shape=shape, dtype=dtype, legacy=True) + assert isinstance(res, dict) + assert prefix in res + # should be dask by default + assert isinstance(res[prefix], dask.array.core.Array) + assert res[prefix].shape == shape - res = read_mds(basename, shape=shape, dtype=dtype, legacy=False) - assert isinstance(res, dict) - assert prefix in res - # should be dask by default - assert isinstance(res[prefix], dask.array.core.Array) - assert res[prefix].shape == (1,) + shape + res = read_mds(basename, shape=shape, dtype=dtype, legacy=False) + assert isinstance(res, dict) + assert prefix in res + # should be dask by default + assert isinstance(res[prefix], dask.array.core.Array) + assert res[prefix].shape == (1,) + shape @pytest.mark.parametrize("method", ["smallchunks", "bigchunks"]) @@ -378,6 +463,22 @@ def test_read_xyz_chunk(all_mds_datadirs, memmap): # function not designed for llc grids, except 1d variables with pytest.raises(ValueError): data = _read_xyz_chunk('T', file_metadata, use_mmap=memmap) + + elif expected['tiled']: + tiled = expected['tiled'] + file_metadata.update({'filename_prefix': dirname + '/' + 'T.' + + str(file_metadata['test_iternum']).zfill(10), + 'vars': ['T'], 'endian': '>', + 'has_faces': False, 'dims_vars': [('nz', 'ny', 'nx')], + 'nz': 2, 'nx': 60, 'ny': 60}) + + if memmap: + with pytest.raises(NotImplementedError): + _read_xyz_chunk('T', file_metadata, use_mmap=memmap, tiled=tiled) + else: + data = _read_xyz_chunk('T', file_metadata, use_mmap=memmap, tiled=tiled) + assert isinstance(data, dask.array.core.Array) + else: file_metadata.update({'nx': file_metadata['shape'][2], 'ny': file_metadata['shape'][1], @@ -401,7 +502,7 @@ def test_read_xyz_chunk(all_mds_datadirs, memmap): 'vars': ['RC'], 'nx': 1, 'ny': 1, 'dims_vars': [('nz', 'ny', 'nx')]}) - data = _read_xyz_chunk('RC', file_metadata, use_mmap=memmap) + data = _read_xyz_chunk('RC', file_metadata, use_mmap=memmap, tiled=False) if memmap: assert isinstance(data, np.memmap) else: @@ -409,11 +510,11 @@ def test_read_xyz_chunk(all_mds_datadirs, memmap): @pytest.mark.parametrize("memmap", [True, False]) -def test_read_xy_chunk(all_mds_datadirs, memmap): +def test_read_xy_chunk(untiled_mds_datadirs, memmap): from xmitgcm.utils import _read_xy_chunk - dirname, expected = all_mds_datadirs + dirname, expected = untiled_mds_datadirs file_metadata = expected file_metadata.update({'filename': dirname + '/' + 'T.' + @@ -490,11 +591,30 @@ def test_read_2D_chunks(all_mds_datadirs, memmap, usedask): dirname, expected = all_mds_datadirs + try: + tiled = expected['tiled'] + except KeyError: + tiled = False + file_metadata = expected file_metadata.update({'filename': dirname + '/' + 'T.' + str(file_metadata['test_iternum']).zfill(10) + '.data', 'vars': ['T'], 'endian': '>'}) # set the size of dimensions (could be changed in _experiments) + if tiled: + file_metadata.update({'filename': dirname + '/' + 'T.' + + str(file_metadata['test_iternum']).zfill(10) + '.001.001' + '.data', 'vars': ['T'], 'endian': '>', + 'filename_prefix': dirname + '/' + 'T.0000000001'}) + + # Check we get the NotImplementedError and continue with our day. + with pytest.raises(NotImplementedError): + data = read_2D_chunks('T', file_metadata, use_mmap=memmap, + use_dask=usedask, tiled=tiled) + + return + + if file_metadata['geometry'] in ['llc']: nx = file_metadata['shape'][3] file_metadata.update({'nx': file_metadata['shape'][3], @@ -557,11 +677,26 @@ def test_read_3D_chunks(all_mds_datadirs, memmap, usedask): dirname, expected = all_mds_datadirs + try: + tiled = expected['tiled'] + except KeyError: + tiled = False + + if tiled and memmap: + # Tiled functions don't currently support memmap so no point testing. + return + file_metadata = expected file_metadata.update({'filename': dirname + '/' + 'T.' + str(file_metadata['test_iternum']).zfill(10) + '.data', 'vars': ['T'], 'endian': '>'}) # set the size of dimensions (could be changed in _experiments) + if tiled: + file_metadata.update({'filename': dirname + '/' + 'T.' + + str(file_metadata['test_iternum']).zfill(10) + '.001.001' + '.data', 'vars': ['T'], 'endian': '>', + 'filename_prefix': dirname + '/' + 'T.0000000001'}) + if file_metadata['geometry'] in ['llc']: nx = file_metadata['shape'][3] file_metadata.update({'nx': file_metadata['shape'][3], @@ -601,12 +736,12 @@ def test_read_3D_chunks(all_mds_datadirs, memmap, usedask): if file_metadata['geometry'] in ['llc', 'cs']: with pytest.raises(ValueError): data = read_3D_chunks('T', file_metadata, use_mmap=memmap, - use_dask=usedask) + use_dask=usedask, tiled=tiled) if usedask: data.compute() else: data = read_3D_chunks('T', file_metadata, use_mmap=memmap, - use_dask=usedask) + use_dask=usedask, tiled=tiled) if usedask: assert isinstance(data, dask.array.core.Array) data.compute() @@ -621,7 +756,7 @@ def test_read_3D_chunks(all_mds_datadirs, memmap, usedask): 'vars': ['RC'], 'nx': 1, 'ny': 1}) data = read_3D_chunks('RC', file_metadata, use_mmap=memmap, - use_dask=usedask) + use_dask=usedask, tiled=False) if usedask: assert isinstance(data, dask.array.core.Array) data.compute() @@ -682,10 +817,13 @@ def test_read_all_variables(all_mds_datadirs, memmap, usedask): dirname, expected = all_mds_datadirs file_metadata = expected + + tiled = expected['tiled'] # test single variable in file file_metadata.update({'filename': dirname + '/' + 'T.' + str(file_metadata['test_iternum']).zfill(10) + '.data', 'vars': ['T'], 'endian': '>'}) + # set the size of dimensions (could be changed in _experiments) if file_metadata['geometry'] in ['llc']: nx = file_metadata['shape'][3] @@ -723,6 +861,14 @@ def test_read_all_variables(all_mds_datadirs, memmap, usedask): [0, 0, 0, 0, 0, 0], 'transpose_face': [False, False, False, False, False, False]}) + elif file_metadata['tiled']: + file_metadata.update({'filename_prefix': dirname + '/' + 'T.' + + str(file_metadata['test_iternum']).zfill(10), + 'vars': ['T'], 'endian': '>', + 'has_faces': False, 'dims_vars': [('nz', 'ny', 'nx')], + 'nt': 1, 'nz': 2, 'nx': 60, 'ny': 60}) + + file_metadata.pop('filename') else: file_metadata.update({'nx': file_metadata['shape'][2], 'ny': file_metadata['shape'][1], @@ -739,6 +885,16 @@ def test_read_all_variables(all_mds_datadirs, memmap, usedask): chunks="3D") if usedask: dataset[0].compute() + elif tiled: + if memmap: + with pytest.raises(NotImplementedError): + dataset = read_all_variables(file_metadata['vars'], file_metadata, + use_mmap=memmap, use_dask=usedask, + chunks="3D", tiled=tiled) + else: + dataset = read_all_variables(file_metadata['vars'], file_metadata, + use_mmap=memmap, use_dask=usedask, + chunks="3D", tiled=tiled) else: dataset = read_all_variables(file_metadata['vars'], file_metadata, use_mmap=memmap, use_dask=usedask, @@ -755,25 +911,31 @@ def test_read_all_variables(all_mds_datadirs, memmap, usedask): assert isinstance(dataset[0], np.ndarray) # test 2D chunks - if file_metadata['geometry'] not in ['cs']: - dataset = read_all_variables(file_metadata['vars'], file_metadata, - use_mmap=memmap, use_dask=usedask, - chunks="2D") + if file_metadata['tiled']: + with pytest.raises(NotImplementedError): + dataset = read_all_variables(file_metadata['vars'], file_metadata, + use_mmap=memmap, use_dask=usedask, + chunks="2D", tiled=tiled) else: - dataset = read_all_variables(file_metadata['vars'], file_metadata, - use_mmap=memmap, use_dask=usedask, - chunks="CS") + if file_metadata['geometry'] not in ['cs']: + dataset = read_all_variables(file_metadata['vars'], file_metadata, + use_mmap=memmap, use_dask=usedask, + chunks="2D") + else: + dataset = read_all_variables(file_metadata['vars'], file_metadata, + use_mmap=memmap, use_dask=usedask, + chunks="CS") - assert isinstance(dataset, list) - assert len(dataset) == len(file_metadata['vars']) - if usedask: - assert isinstance(dataset[0], dask.array.core.Array) - else: - if memmap: - # should be memmap, needs fix - assert isinstance(dataset[0], np.ndarray) + assert isinstance(dataset, list) + assert len(dataset) == len(file_metadata['vars']) + if usedask: + assert isinstance(dataset[0], dask.array.core.Array) else: - assert isinstance(dataset[0], np.ndarray) + if memmap: + # should be memmap, needs fix + assert isinstance(dataset[0], np.ndarray) + else: + assert isinstance(dataset[0], np.ndarray) # test multiple variables in file # those tests are only available for llc experiment: @@ -789,20 +951,26 @@ def test_read_all_variables(all_mds_datadirs, memmap, usedask): 'vars': expected['diagnostics'][1], 'dims_vars': dimsvar}) - dataset = read_all_variables(file_metadata['vars'], file_metadata, - use_mmap=memmap, use_dask=usedask, - chunks="2D") + if not expected['tiled']: + dataset = read_all_variables(file_metadata['vars'], file_metadata, + use_mmap=memmap, use_dask=usedask, + chunks="2D") + elif expected['tiled'] and not memmap: + dataset = read_all_variables(file_metadata['vars'], file_metadata, + use_mmap=memmap, use_dask=usedask, + chunks="3D", tiled=tiled) - assert isinstance(dataset, list) - assert len(dataset) == len(file_metadata['vars']) - if usedask: - assert isinstance(dataset[0], dask.array.core.Array) - else: - if memmap: - # should be memmap, needs fix - assert isinstance(dataset[0], np.ndarray) + if not (expected['tiled'] and memmap): + assert isinstance(dataset, list) + assert len(dataset) == len(file_metadata['vars']) + if usedask: + assert isinstance(dataset[0], dask.array.core.Array) else: - assert isinstance(dataset[0], np.ndarray) + if memmap: + # should be memmap, needs fix + assert isinstance(dataset[0], np.ndarray) + else: + assert isinstance(dataset[0], np.ndarray) @pytest.mark.parametrize("dtype", ['>d', '>f', '>i']) @@ -905,10 +1073,10 @@ def test_pad_array(tmpdir, memmap, dtype): assert data_padded[1, 1] == 4 -def test_parse_diagnostics(all_mds_datadirs, layers_mds_datadirs): +def test_parse_diagnostics(untiled_mds_datadirs, layers_mds_datadirs): """Make sure we can parse the available_diagnostics.log file.""" from xmitgcm.utils import parse_available_diagnostics - dirname, expected = all_mds_datadirs + dirname, expected = untiled_mds_datadirs diagnostics_fname = os.path.join(dirname, 'available_diagnostics.log') ad = parse_available_diagnostics(diagnostics_fname)