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import os
import numpy as np
import pytest
from nexusformat.nexus.tree import (NXentry, NXfield, NXgroup, NXlink, NXroot,
nxload, nxsetlock)
@pytest.fixture
def field1a(): return NXfield((1, 2), name="f1", dtype=np.float32, units='m')
@pytest.fixture
def field2a(): return NXfield((3, 4), name="f2", dtype=np.int16)
def test_link_creation(field1a):
root = NXroot()
root["g1"] = NXgroup(f1=field1a)
root["g2"] = NXgroup()
root["g2"].f1_link = NXlink(root["g1/f1"])
assert "g1/f1" in root
assert "g2/f1_link" in root
assert root["g2/f1_link"].nxlink == root["g1/f1"]
assert root["g2/f1_link"].nxtarget == "/g1/f1"
root["g2/f2_link"] = NXlink(target="/g1/f1")
assert root["g2/f2_link"].nxlink == root["g1/f1"]
root["g2"].makelink(root["g1/f1"], name="f3_link")
assert root["g2/f3_link"].nxlink == root["g1/f1"]
@pytest.mark.parametrize("save", ["False", "True"])
def test_saved_links(tmpdir, field1a, save):
root = NXroot()
root["g1"] = NXgroup(f1=field1a)
root["g2"] = NXgroup()
filename = os.path.join(tmpdir, "file1.nxs")
root.save(filename, mode="w")
root["g2"].f1_link = NXlink(root["g1/f1"])
if save:
root = nxload(filename, "rw")
assert root["g2/f1_link"].shape == (2,)
assert root["g2/f1_link"].dtype == np.float32
root["g1/f1"].attrs["a1"] = 1
assert "a1" in root["g2/f1_link"].attrs
assert root["g2/f1_link"].a1 == 1
assert root["g2/f1_link"].nxdata[0] == root["g1/f1"].nxdata[0]
@pytest.mark.parametrize("save", ["False", "True"])
def test_linkfield_properties(tmpdir, field1a, save):
root = NXroot()
root["g1"] = NXgroup(f1=field1a)
root["g2"] = NXgroup()
root["g2"].f1_link = NXlink(root["g1/f1"])
if save:
filename = os.path.join(tmpdir, "file1.nxs")
root.save(filename, mode="w")
assert root["g2/f1_link"].shape == (2,)
assert root["g2/f1_link"].dtype == np.float32
root["g1/f1"].attrs["a1"] = 1
assert "a1" in root["g2/f1_link"].attrs
assert root["g2/f1_link"].a1 == 1
assert root["g2/f1_link"].nxdata[0] == root["g1/f1"].nxdata[0]
@pytest.mark.parametrize("save", ["False", "True"])
def test_linkgroup_properties(tmpdir, field1a, save):
root = NXroot(NXentry())
root["entry/g1"] = NXgroup()
root["entry/g1/g2"] = NXgroup(field1a)
root["entry/g2_link"] = NXlink("/entry/g1/g2")
if save:
filename = os.path.join(tmpdir, "file1.nxs")
root.save(filename, mode="w")
root = nxload(filename)
assert "f1" in root["entry/g2_link"]
assert len(root["entry/g2_link"]) == len(root["entry/g1/g2"])
assert root["entry/g2_link"].nxtarget == "/entry/g1/g2"
assert root["entry/g1/g2/f1"].nxroot is root
assert root["entry/g1/g2/f1"].nxgroup is root["entry/g2_link"].nxlink
assert root["entry/g2_link"].nxroot is root
assert root["entry/g2_link"].nxgroup is root["entry"]
assert root["entry/g2_link"].nxlink.entries == root["entry/g1/g2"].entries
@pytest.mark.parametrize("save", ["False", "True"])
def test_embedded_links(tmpdir, save, field1a, field2a):
root = NXroot(NXentry())
root["entry/g1"] = NXgroup()
root["entry/g1/g2"] = NXgroup()
root["entry/g1/g2/g3"] = NXgroup(field1a)
root["entry/g2_link"] = NXlink("/entry/g1/g2")
if save:
filename = os.path.join(tmpdir, "file1.nxs")
root.save(filename, mode="w")
root = nxload(filename, "rw")
assert "f1" in root["entry/g2_link/g3"]
assert not root["entry/g2_link"].is_linked()
assert root["entry/g2_link/g3"].is_linked()
assert root["entry/g2_link/g3/f1"].is_linked()
assert len(root["entry/g2_link/g3"]) == len(root["entry/g1/g2/g3"])
assert root["entry/g2_link/g3/f1"].nxpath == "/entry/g2_link/g3/f1"
assert root["entry/g2_link/g3/f1"].nxfilepath == "/entry/g1/g2/g3/f1"
assert root["entry/g2_link/g3/f1"].nxroot is root
assert root["entry/g2_link/g3/f1"].nxgroup.nxgroup is root["entry/g2_link"]
root["entry/g1/g2/g3/f1"] = [7, 8]
root["entry/g1/g2/g3/f1"].attrs["a"] = 1
assert root["entry/g2_link/g3/f1"][0] == 7
assert "a" in root["entry/g2_link/g3/f1"].attrs
assert root["entry/g2_link/g3/f1"].attrs["a"] == 1
root["entry/g1/g2/g3/f2"] = field2a
assert "f2" in root["entry/g2_link/g3"]
del root["entry/g1/g2/g3/f2"]
assert "f2" not in root["entry/g2_link/g3"]
@pytest.mark.parametrize("save", ["False", "True"])
def test_external_field_links(tmpdir, field1a, save):
root = NXroot(NXentry())
if save:
filename = os.path.join(tmpdir, "file1.nxs")
root.save(filename, mode="w")
external_filename = os.path.join(tmpdir, "file2.nxs")
external_root = NXroot(NXentry(field1a))
external_root.save(external_filename, mode="w")
root["entry/f1_link"] = NXlink(target="/entry/f1", file=external_filename)
assert root["entry/f1_link"].nxtarget == "/entry/f1"
assert root["entry/f1_link"].nxfilepath == "/entry/f1"
assert root["entry/f1_link"].nxfilename == external_filename
assert root["entry/f1_link"].nxfilemode == "r"
assert root["entry/f1_link"].nxroot == root
assert root["entry/f1_link"].nxgroup == root["entry"]
assert root["entry/f1_link"].file_exists()
assert root["entry/f1_link"].path_exists()
assert root["entry/f1_link"].shape == external_root["entry/f1"].shape
assert root["entry/f1_link"][0] == external_root["entry/f1"][0]
assert "units" in root["entry/f1_link"].attrs
@pytest.mark.parametrize("save", ["False", "True"])
def test_external_group_links(tmpdir, field1a, save):
root = NXroot(NXentry())
if save:
filename = os.path.join(tmpdir, "file1.nxs")
root.save(filename, mode="w")
external_filename = os.path.join(tmpdir, "file2.nxs")
external_root = NXroot(
NXentry(NXgroup(field1a, name='g1', attrs={"a": "b"})))
external_root.save(external_filename, mode="w")
root["entry/g1_link"] = NXlink(target="/entry/g1", file=external_filename)
assert root["entry/g1_link"].nxtarget == "/entry/g1"
assert root["entry/g1_link"].nxfilepath == "/entry/g1"
assert root["entry/g1_link"].nxfilename == external_filename
assert root["entry/g1_link"].nxfilemode == "r"
assert root["entry/g1_link"].nxroot == root
assert root["entry/g1_link"].nxgroup == root["entry"]
assert root["entry/g1_link"].file_exists()
assert root["entry/g1_link"].path_exists()
assert "f1" in root["entry/g1_link"]
assert root["entry/g1_link/f1"].nxfilename == (
root["entry/g1_link"].nxfilename)
assert root["entry/g1_link/f1"].nxfilepath == "/entry/g1/f1"
assert root["entry/g1_link/f1"].nxroot == root
assert root["entry/g1_link/f1"].nxgroup is root["entry/g1_link"]
assert root["entry/g1_link/f1"][0] == external_root["entry/g1/f1"][0]
assert "a" in root["entry/g1_link"].attrs
assert "units" in root["entry/g1_link/f1"].attrs
def test_external_group_files(tmpdir, field1a):
nxsetlock(10)
filename = os.path.join(tmpdir, "file1.nxs")
root = NXroot(NXentry())
root.save(filename, mode="w")
external_filename = os.path.join(tmpdir, "file2.nxs")
external_root = NXroot(
NXentry(NXgroup(field1a, name='g1', attrs={"a": "b"})))
external_root.save(external_filename, mode="w")
root["entry/g1_link"] = NXlink(target="/entry/g1", file=external_filename)
with root.nxfile:
assert root.nxfile.filename == filename
assert root.nxfile.locked
with root["entry/g1_link"].nxfile:
assert root["entry/g1_link"].nxfile.filename == external_filename
assert root["entry/g1_link"].nxfile.locked
assert root.nxfile.locked
assert not root["entry/g1_link"].nxfile.locked
assert not root.nxfile.locked
@pytest.mark.parametrize("save", ["False", "True"])
def test_soft_field_links(tmpdir, field1a, field2a, save):
root = NXroot()
root["g1"] = NXgroup()
root["g1/g2"] = NXgroup(f1=field1a, f2=field2a)
root["g1/f1_link"] = NXlink(target="g1/g2/f1", soft=True)
root["g1/f2_link"] = NXlink(target="g1/g2/f2", soft=True)
if save:
filename = os.path.join(tmpdir, "file1.nxs")
root.save(filename, mode="w")
assert root["g1/f1_link"].shape == (2,)
assert root["g1/f1_link"].dtype == np.float32
root["g1/g2/f1"].attrs["a1"] = 1
assert "a1" in root["g1/f1_link"].attrs
assert root["g1/f1_link"].a1 == 1
assert root["g1/f1_link"].nxdata[0] == root["g1/g2/f1"].nxdata[0]
assert root["g1/f2_link"].shape == (2,)
assert root["g1/f2_link"].dtype == np.int16
root["g1/g2/f2"].attrs["a2"] = 2
assert "a2" in root["g1/f2_link"].attrs
assert root["g1/f2_link"].a2 == 2
assert root["g1/f2_link"].nxdata[0] == root["g1/g2/f2"].nxdata[0]
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