def setUp(self):
self.gf = open_file(self.full_path,readonly=False)
self.root = self.gf.root()
self.generator = random_generator_factory(self._typecode)
self.input_data = next(self.generator())
self.input_array_data = numpy.array([next(self.generator())])
self.scalar_type = iotu.scalars[self._typecode]
def test_read_only(self):
"""
Open a single file in read only mode.
"""
f = open_file(self.full_path)
self.assertTrue(f.readonly)
r = f.root()
self.assertRaises(ObjectError,r.create_group,"entry","NXentry")
def test_read_write(self):
"""
Open a single file in read-write mode.
"""
f = open_file(self.full_path,readonly=False)
self.assertFalse(f.readonly)
r = f.root()
r.create_group("entry","NXentry")
def open_file(filename, readonly=False, libver=None):
""" open the new file
:param filename: file name
:type filename: :obj:`str`
:param readonly: readonly flag
:type readonly: :obj:`bool`
:param libver: library version: 'lastest' or 'earliest'
:type libver: :obj:`str`
:returns: file object
:rtype: :class:`PNIFile`
"""
return PNIFile(nx.open_file(filename, readonly), filename)
def reopen(self, readonly=False, swmr=False, _=None):
""" reopen file
:param readonly: readonly flag
:type readonly: :obj:`bool`
:param swmr: swmr flag
:type swmr: :obj:`bool`
:param libver: library version, default: 'latest'
:type libver: :obj:`str`
"""
if swmr:
raise Exception("SWMR not supported")
self._h5object = nx.open_file(self.name, readonly)
filewriter.FTFile.reopen(self)
def test_link_field_from_path(self):
os.chdir(os.path.dirname(os.path.abspath(__file__)))
f = nexus.open_file(self.master2_full_path,readonly=False)
r = f.root()
detector_group = nexus.get_object(r,"/:NXentry/:NXinstrument/:NXdetector")
nexus.link("external_link_test_detector.nxs://entry/instrument/mca/data",
detector_group,"mca_data")
d = detector_group["mca_data"]
self.assertEqual(d.name,"data")
self.assertEqual(d.path,"/entry:NXentry/instrument:NXinstrument/mca:NXdetector/data")
data = nexus.get_object(r,"/:NXentry/:NXdata")
d = data["plot_data"]
def test_link_group_from_path(self):
"""
Test link creation from a path. The target is only specified by its
path.
"""
os.chdir(os.path.dirname(os.path.abspath(__file__)))
f = nexus.open_file(self.master1_full_path,readonly=False)
r = f.root()
instrument_group = nexus.get_object(r,"/:NXentry/:NXinstrument")
nexus.link("external_link_test_detector.nxs://entry/instrument/mca",
instrument_group,"detector")
d = instrument_group["detector"]
self.assertEqual(d.name,"mca")
self.assertEqual(d.path,"/entry:NXentry/instrument:NXinstrument/mca:NXdetector")
data = nexus.get_object(r,"/:NXentry/:NXdata")
d = data["plot_data"]
def setUp(self):
self.gf = open_file(self.full_path,readonly=False)
self.root = self.gf.root()
self.generator = random_generator_factory(self._typecode)
self.scalar_type = iotu.scalars[self._typecode]
self.field = self.root["data"]
def setUp(self):
self.gf = open_file(self.full_path,readonly=False)
self.root = self.gf.root()
from __future__ import print_function
import pni.io.nx.h5 as nx
import numpy
f = nx.create_file("test_attributes.nxs",True)
r = f.root()
a = r.attributes.create("test_scalar","string")
a[...] = "hello world"
a = r.attributes.create("test_array","string",shape=(2,3))
data = numpy.array([["hello","world","this"],["is","a","test"]])
print(data)
print(data.dtype)
a[...] = data
a.close()
r.close()
f.close()
f = nx.open_file("test_attributes.nxs")
r = f.root()
a = r.attributes["test_scalar"]
print(a[...])
a = r.attributes["test_array"]
print(a[...])
print(a[...].flat[...])
#!/usr/bin/env python
#file: nxfile_ex2.py
import pni.io.nx.h5 as nexus
fname = "nxfile_ex2.nxs"
try:
print "try to open an existing file ..."
nxfile = nexus.open_file(fname)
except:
print "Error opening file - recreate ..."
nxfile = nexus.create_file(fname,overwrite=True)
nxfile.close()
from __future__ import print_function
import pni.io.nx.h5 as nx
import numpy
f = nx.create_file("test_fields.nxs",True)
r = f.root()
field = r.create_field("test_scalar","string")
field[...] = "hello world"
field = r.create_field("test_array","string",shape=(2,3))
data = numpy.array([["hello","world","this"],["is","a","test"]])
print(data)
print(data.dtype)
field[...] = data
field.close()
r.close()
f.close()
f = nx.open_file("test_fields.nxs",False)
r = f.root()
field = r["test_scalar"]
print(field[...])
field = r["test_array"]
print(field[...])
from __future__ import print_function
import pni.io.nx.h5 as nx
f = nx.create_file("test.nxs",overwrite=True)
f.close()
f = nx.open_file("test.nxs")
print(f.readonly)
f.close()
f = nx.open_file("test.nxs",readonly=False)
print(f.readonly)
f.close()
from __future__ import print_function
import numpy
import pni.io.nx.h5 as nexus
#open the file
det_path = "/:NXentry/:NXinstrument/:NXdetector/data"
f = nexus.open_file("image_writer.nxs")
data = nexus.get_object(f.root(),det_path)
for index in range(data.shape[0]):
if numpy.equal(data[index,...],
index*numpy.ones((data.shape[1],data.shape[2]),dtype=data.dtype)).all():
print("fame {frame_index} is ok".format(frame_index=index))
from __future__ import print_function
import pni.io.nx.h5 as nx
import numpy
f = nx.create_file("test.nxs", True)
r = f.root()
a = r.attributes.create("test_scalar", "string")
a[...] = "hello world"
a = r.attributes.create("test_array", "string", shape=(2, 3))
data = numpy.array([["hello", "world", "this"], ["is", "a", "test"]])
print(data)
print(data.dtype)
a[...] = data
a.close()
r.close()
f.close()
f = nx.open_file("test.nxs")
r = f.root()
a = r.attributes["test_scalar"]
print(a.value)
a = r.attributes["test_array"]
print(a.value)
