def test_group_with_dataset(tmp_path):
md = {
"entry": {
"_attributes": {
"NX_Class": "NXEntry",
"default": "data"
},
"program_name": "EPICS areaDetector",
}
}
filepath = tmp_path / Path("test.h5")
with h5py.File(filepath, "w") as f:
_copy_nexus_md_to_nexus_h5(nexus_md=md, h5_group_or_dataset=f)
with h5py.File(filepath, "r") as f:
# expect this structure:
# /<group "entry">
# <attr "NX_Class": "NXEntry">
# <attr "default": "data">
# <dataset "program_name": "EPICS areaDetector">
assert len(f) == 1
assert "entry" in f
assert len(f["entry"].attrs) == 2
assert f["entry"].attrs["NX_Class"] == "NXEntry"
assert f["entry"].attrs["default"] == "data"
assert "program_name" in f["entry"]
assert isinstance(f["entry"]["program_name"], h5py.Dataset)
assert f["entry"]["program_name"][()] == "EPICS areaDetector"
def test_group_with_attributes(tmp_path):
md = {"entry": {"_attributes": {"NX_Class": "NXEntry", "default": "data"}}}
filepath = tmp_path / Path("test.h5")
with h5py.File(filepath, "w") as f:
_copy_nexus_md_to_nexus_h5(nexus_md=md, h5_group_or_dataset=f)
with h5py.File(filepath, "r") as f:
# expect this structure:
# /<group "entry">
# <attr "NX_Class": "NXEntry">
# <attr "default": "data">
assert len(f) == 1
assert "entry" in f
assert len(f["entry"].attrs) == 2
assert f["entry"].attrs["NX_Class"] == "NXEntry"
assert f["entry"].attrs["default"] == "data"
def test_group_with_dataset_link(tmp_path):
md = {
"entry": {
"_attributes": {
"NX_Class": "NXEntry",
"default": "data"
},
"GUPNumber": "#bluesky/start/gup_number",
}
}
filepath = tmp_path / Path("test.h5")
with h5py.File(filepath, "w") as f:
# create a target dataset for #bluesky/start/gup_number
f.create_group("bluesky").create_group("start").create_dataset(
name="gup_number", data=1)
_copy_nexus_md_to_nexus_h5(nexus_md=md, h5_group_or_dataset=f)
with h5py.File(filepath, "r") as f:
# expect this structure:
# /<group "bluesky">
# <group "start">
# <dataset "gup_number": 1>
# /<group "entry">
# <attr "NX_Class": "NXEntry">
# <attr "default": "data">
# <link "GUPNumber" <dataset bluesky/start/gup_number>>
assert len(f) == 2
assert "bluesky" in f
assert "start" in f["bluesky"]
assert "gup_number" in f["bluesky"]["start"]
assert f["bluesky"]["start"]["gup_number"][()] == 1
assert "entry" in f
assert len(f["entry"].attrs) == 2
assert f["entry"].attrs["NX_Class"] == "NXEntry"
assert f["entry"].attrs["default"] == "data"
assert "GUPNumber" in f["entry"]
assert isinstance(f["entry"]["GUPNumber"], h5py.Dataset)
assert f["entry"]["GUPNumber"][()] == 1
assert f["entry"]["GUPNumber"] == f["bluesky"]["start"]["gup_number"]
def test_group_with_subgroup(tmp_path):
md = {
"entry": {
"_attributes": {
"NX_Class": "NXEntry",
"default": "data"
},
"instrument": {
"_attributes": {
"NX_Class": "NXInstrument"
},
"name_1": "#bluesky/start/beamline_id",
"name_2": {
"_attributes": {
"NX_This": "NXThat"
},
"_link": "#bluesky/start/beamline_id",
},
},
},
}
filepath = tmp_path / Path("test.h5")
with h5py.File(filepath, "w") as f:
# create a target dataset for #bluesky/start/gup_number
f.create_group("bluesky").create_group("start").create_dataset(
name="beamline_id", data="RSOXS")
_copy_nexus_md_to_nexus_h5(nexus_md=md, h5_group_or_dataset=f)
with h5py.File(filepath, "r") as f:
# expect this structure:
# /<group "bluesky">
# <group "start">
# <dataset "gup_number": 1>
# /<group "entry">
# <attr "NX_Class": "NXEntry">
# <attr "default": "data">
# <dataset "name_1": "">
# <link "GUPNumber" <dataset bluesky/start/gup_number>>
# <attr "NDAttrDescription": "GUP proposal number">
# <attr "NDAttrName": "GUPNumber">
# <attr "NDAttrSource": "91dcLAX:GUPNumber">
# <attr "NDAttrSourceType": "NDAttrSourceEPICSPV">
assert len(f) == 2
def test(tmp_path):
md = {
"techniques": [
# SAXS technique
{
"version": 1,
"technique": "SAXS",
"nxsas": {
"entry": {
"_attributes": {
"NX_Class": "NXEntry",
"default": "data"
},
"instrument": {
"_attributes": {
"NX_Class": "NXInstrument"
},
"name": "#bluesky/start/beamline_id",
"aperture": {
"_attributes": {
"NX_Class": "NXAperture"
},
"vcenter": 1.0,
"vsize": 2.0,
"description": "USAXSslit",
},
},
},
},
},
# more techniques ...
]
}
filepath = tmp_path / Path("test.h5")
with h5py.File(filepath, "w") as f:
f.create_group("bluesky").create_group("start").create_dataset(
name="beamline_id", data="SST-1 RSoXS")
_copy_nexus_md_to_nexus_h5(nexus_md=md["techniques"][0]["nxsas"],
h5_group_or_dataset=f)
with h5py.File(filepath, "r") as f:
print(list(f))
assert "entry" in f
print(list(f["entry"]))
entry_h5_group = f["entry"]
assert len(entry_h5_group.attrs) == 2
assert entry_h5_group.attrs["NX_Class"] == "NXEntry"
assert entry_h5_group.attrs["default"] == "data"
assert "instrument" in entry_h5_group
assert len(entry_h5_group["instrument"].attrs) == 1
assert entry_h5_group["instrument"].attrs["NX_Class"] == "NXInstrument"
# what does [()] mean?
print(entry_h5_group["instrument"]["name"])
assert entry_h5_group["instrument"]["name"][()] == "SST-1 RSoXS"
assert "aperture" in entry_h5_group["instrument"]
assert len(entry_h5_group["instrument"]["aperture"].attrs) == 1
assert (entry_h5_group["instrument"]["aperture"].attrs["NX_Class"] ==
"NXAperture")
assert entry_h5_group["instrument"]["aperture"]["vcenter"][()] == 1.0
assert entry_h5_group["instrument"]["aperture"]["vsize"][()] == 2.0
assert (entry_h5_group["instrument"]["aperture"]["description"][(
)] == "USAXSslit")
def test_dataset_with_attributes(tmp_path):
md = {
"entry": {
"_attributes": {
"NX_Class": "NXEntry",
"default": "data"
},
"GUPNumber": {
"_attributes": {
"NDAttrDescription": "GUP proposal number",
"NDAttrName": "GUPNumber",
},
"_data": 123,
},
"ProgramName": {
"_attributes": {
"NDAttrDescription": "Program Name",
"NDAttrName": "ProgramName",
},
"_data": "the name of the program",
}
}
}
filepath = tmp_path / Path("test.h5")
with h5py.File(filepath, "w") as f:
_copy_nexus_md_to_nexus_h5(nexus_md=md, h5_group_or_dataset=f)
with h5py.File(filepath, "r") as f:
# expect this structure:
# /<group "entry">
# <attr "NX_Class": "NXEntry">
# <attr "default": "data">
# <dataset "GUPNumber" <123>>
# <attr "NDAttrDescription": "GUP proposal number">
# <attr "NDAttrName": "GUPNumber">
# <dataset "ProgramName" <"the name of the program">>
# <attr "NDAttrDescription": "Program Name">
# <attr "NDAttrName": "ProgramName">
assert len(f) == 1
# assert "bluesky" in f
# assert "start" in f["bluesky"]
# assert "gup_number" in f["bluesky"]["start"]
# assert f["bluesky"]["start"]["gup_number"][()] == 123
assert "entry" in f
assert len(f["entry"].attrs) == 2
assert f["entry"].attrs["NX_Class"] == "NXEntry"
assert f["entry"].attrs["default"] == "data"
assert "GUPNumber" in f["entry"]
assert isinstance(f["entry"]["GUPNumber"], h5py.Dataset)
assert f["entry"]["GUPNumber"][()] == 123
assert len(f["entry"]["GUPNumber"].attrs) == 2
assert (f["entry"]["GUPNumber"].attrs["NDAttrDescription"] ==
"GUP proposal number")
assert f["entry"]["GUPNumber"].attrs["NDAttrName"] == "GUPNumber"
assert "ProgramName" in f["entry"]
assert isinstance(f["entry"]["ProgramName"], h5py.Dataset)
assert f["entry"]["ProgramName"][()] == "the name of the program"
assert len(f["entry"]["ProgramName"].attrs) == 2
assert (f["entry"]["ProgramName"].attrs["NDAttrDescription"] ==
"Program Name")
assert f["entry"]["ProgramName"].attrs["NDAttrName"] == "ProgramName"
