def load(self, warn=True):
# capture all error messages
oldErr = _system.err
_system.setErr(_pstream(_NoOutputStream()))
try:
jdh = self._loadFile()
finally:
_system.setErr(oldErr)
data = asDatasetList(jdh.getList())
names = jdh.getNames()
basenames = []
from os import path as _path
for n in names: # remove bits of path so sanitising works
if _path.exists(n):
basenames.append(_path.basename(n))
else:
basenames.append(n)
if len(data) != len(basenames):
raise io_exception, "Number of names does not match number of datasets"
metadata = None
if self.load_metadata:
meta = jdh.getMetadata()
if meta:
mnames = meta.metaNames
if mnames:
metadata = [(k, meta.getMetaValue(k)) for k in mnames]
return DataHolder(zip(basenames, data), metadata, warn)
def createSimpleScanFileHolderAndScannables():
w = MockScannable('w', ['wi1', 'wi2'], ['we'])
x = MockScannable('x', ['x'], [])
y = MockScannable('y', ['yi'], ['ypath', 'ye'])
y.outputformats = ['%.2f', '%s', '%.2f']
z = MockScannable('z', [], ['ze1', 'ze2'])
# Using DataHolder to replace deprecated ScanFileHolder
testData = DataHolder()
testData['x'] = [0., 1., 2., 3., 4., 5., 6., 7., 8., 9.]
testData['yi'] = [0, .1, .2, .3, .4, .5, .3, .2, .1, 0.]
testData['ye'] = [1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.3, 1.2, 1.1, 1.0]
testData['ze1'] = [0., 10., 20., 30., 40., 50., 60., 70., 80., 90.]
testData['ze2'] = [1., 11., 21., 31., 41., 51., 61., 71., 81., 91.]
testData['wi1'] = [
100., 101., 102., 103., 104., 105., 106., 107., 108., 109.
]
testData['wi2'] = [
100., 101., 102., 103., 104., 105., 104., 103., 102., 101., 100.
]
testData['we'] = [
100., 100.1, 100.2, 100.3, 100.4, 100.5, 100.3, 100.2, 100.1, 100.0
]
return w, x, y, z, testData
def load(self, warn=True):
# py4j gymnastics to get access to Java LoaderFactory
from . import py4jutils as utils #@UnresolvedImport
try:
java = utils.get_gateway().jvm
except:
raise io_exception("No Py4J gateway so cannot use Java loaders")
loader_factory = java.uk.ac.diamond.scisoft.analysis.io.LoaderFactory
jdh = loader_factory.getData(self.name, self.load_metadata, None)
# convert to Python
data = utils.convert_datasets(jdh.getList())
names = jdh.getNames()
basenames = []
from os import path as _path
for n in names: # remove bits of path so sanitising works
if _path.exists(n):
basenames.append(_path.basename(n))
else:
basenames.append(n)
if len(data) != len(basenames):
raise io_exception("Number of names does not match number of datasets")
metadata = None
if self.load_metadata:
meta = jdh.getMetadata()
if meta:
mnames = meta.getMetaNames()
if mnames:
mnames = java.java.util.ArrayList(mnames) # make it iterable
metadata = [ (k, meta.getMetaValue(k)) for k in mnames if k is not None ]
return DataHolder(list(zip(basenames, data)), metadata, warn)
def load(self, warn=True):
if _tf is None:
raise NotImplementedError
data = []
if self.load_metadata:
metadata = dict()
else:
metadata = None
t = _tf.TiffFile(self.name)
for i, p in enumerate(t.pages):
d = p.asarray()
if p.photometric == p.photometric.RGB:
# convert to an rgb dataset
d = _core.asarray(d, dtype=_core.int16).view(_RGB)
if not self.ascolour:
d = d.get_grey()
data.append(("image-%02d" % (i+1,), d))
if self.load_metadata:
for k,v in p.tags.items():
metadata[k] = v.value
if len(data) < 1:
pass
return DataHolder(data, metadata, warn)
def load(self, warn=True):
import numpy as np #@UnresolvedImport
d = np.load(self.name)
import os.path as _path
n = self.name
if _path.exists(n):
n = _path.basename(n)
return DataHolder([(n, d)], warn=warn)
def load(self, warn=True):
'''
warn -- if True (default), print warnings about key names
Returns a DataHolder object
'''
f = open(self.name)
try:
hdrtext = []
while True:
l = f.readline()
if not l:
raise io_exception("End of file reached unexpectedly")
ls = l.strip()
if ls:
if _begin_number.match(ls):
break
if ls.startswith("#"):
if self.load_metadata:
ls = ls[1:].strip()
if ls:
hdrtext.append(ls)
else:
raise io_exception("No end tag found")
colstext = hdrtext.pop().strip() if hdrtext else None
datatext = [ls]
while True:
l = f.readline()
if l:
ls = l.strip()
if ls.startswith("#"):
if self.load_metadata:
ls = ls[1:].strip()
if ls:
hdrtext.append(ls)
elif _begin_number.match(ls):
datatext.append(ls)
else:
break
data = self._parse_data(colstext, datatext, warn)
metadata = self._parse_head(hdrtext, warn)
return DataHolder(data, metadata, warn)
finally:
f.close()
def createSimpleScanFileHolderWithOneValueAndScannables():
w = MockScannable('w', ['wi1', 'wi2'], ['we'])
x = MockScannable('x', ['x'], [])
y = MockScannable('y', ['yi'], ['ye'])
z = MockScannable('z', [], ['ze1', 'ze2'])
# Using DataHolder to replace deprecated ScanFileHolder
testData = DataHolder()
testData['x'] = [0.]
testData['yi'] = [1.]
testData['ye'] = [2.]
testData['ze1'] = [3.]
testData['ze2'] = [4.]
testData['wi1'] = [5.]
testData['wi2'] = [6.]
testData['we'] = [7.]
return w, x, y, z, testData
def load(self, warn=True):
if _im is None:
raise NotImplementedError
im = _im.open(self.name)
if im.mode == 'RGB':
if self.ascolour:
# convert to an rgb dataset
d = _core.asarray(im, dtype=_core.int16).view(_RGB)
else:
im = im.convert('L')
d = _core.asarray(im)
else:
d = _core.asarray(im)
import os.path as _path
n = self.name
if _path.exists(n):
n = _path.basename(n)
return DataHolder([(n, d)], warn=warn)
def load(self, warn=True):
data = []
metadata = []
try:
h = _cbf.cbf_handle_struct()
h.read_widefile(self.name, _cbf.MSG_DIGEST)
h.rewind_datablock()
for nd in range(h.count_datablocks()):
h.select_datablock(nd)
# db_name = h.datablock_name()
# print "DBl: %d, %s" % (nd, db_name)
h.rewind_category()
for nc in range(h.count_categories()):
h.select_category(nc)
# ct_name = h.category_name()
# print " Cat: %d, %s" % (nc, ct_name)
h.rewind_column()
colnames = []
for nv in range(h.count_columns()):
h.select_column(nv)
cl_name = h.column_name()
colnames.append(cl_name)
# print " Col: %d, %s" % (nv, cl_name)
h.rewind_row()
for nh in range(h.count_rows()):
h.select_row(nh)
h.rewind_column()
for nv in range(h.count_columns()):
h.select_column(nv)
v = self.getvalue(h)
# print " %d %d: " % (nh, nv), v
item = "%s-%d" % (colnames[nv], nh), v
if isinstance(v, numpy.ndarray):
data.append(item)
else:
metadata.append(item)
finally:
del(h)
return DataHolder(data, metadata, warn)
def load(self, warn=True):
'''
warn -- if True (default), print warnings about key names
Returns a DataHolder object
'''
f = open(self.name)
try:
header = False
while True:
l = f.readline()
if not l:
raise io_exception("End of file reached unexpectedly")
ls = l.lstrip()
if ls.startswith("&SRS") or ls.startswith("&DLS"):
header = True
break
if _begin_number.match(ls):
break
else:
raise io_exception("Not an SRS file")
srstext = []
if header:
while True:
l = f.readline()
if not l:
raise io_exception("End of file reached unexpectedly")
ls = l.strip()
if ls:
if ls.startswith("&END"):
break
if self.load_metadata:
srstext.append(ls)
else:
raise io_exception("No end tag found")
l = f.readline()
if not l:
raise io_exception("End of file reached unexpectedly")
colstext = l.strip()
datatext = []
else:
colstext = None
datatext = [ls]
while True:
l = f.readline()
if not l:
break
ls = l.lstrip()
if _begin_number.match(ls):
datatext.append(ls)
else:
break
data = SRSLoader._parse_data(colstext, datatext, warn)
metadata = SRSLoader._parse_head(srstext, warn)
return DataHolder(data, metadata, warn)
finally:
f.close()
