def testExportChronogram(self):
"""Try simple chronogram export"""
size = (150, )
dtype = numpy.uint16
md = {
model.MD_TIME_LIST: numpy.linspace(536e-9, 650e-9,
size[0]).tolist(),
model.MD_ACQ_TYPE: model.MD_AT_SPECTRUM,
model.MD_DIMS: "T"
}
data = model.DataArray(numpy.zeros(size, dtype), md)
data += 56
# export
csv.export(FILENAME, data)
# check it's here
st = os.stat(FILENAME) # this test also that the file is created
self.assertGreater(st.st_size, 150)
raised = False
try:
pycsv.reader(open(FILENAME, 'rb'))
except IOError:
raised = True
self.assertFalse(raised, 'Failed to read csv file')
def testExportAR(self):
"""Try simple AR export"""
size = (101, 401)
dtype = numpy.float
metadata = {
model.MD_DESCRIPTION: "Angle-resolved",
model.MD_ACQ_TYPE: model.MD_AT_AR
}
data = model.DataArray(numpy.zeros(size, dtype), metadata)
data += 26.1561
data[1:, 0] = numpy.linspace(0, math.pi / 2, data.shape[0] - 1)
data[0, 1:] = numpy.linspace(0, math.pi * 2, data.shape[1] - 1)
# export
csv.export(FILENAME, data)
# check it's here
st = os.stat(FILENAME) # this test also that the file is created
self.assertGreater(st.st_size, 100)
raised = False
try:
pycsv.reader(open(FILENAME, 'rb'))
except IOError:
raised = True
self.assertFalse(raised, 'Failed to read csv file')
def export_ar_to_csv(fn, background=None):
"""
fn (str): full path to the AR data file
background (DataArray or None): background data to subtract
"""
das = dataio.open_acquisition(fn)
if not das: # No such file or file doesn't contain data
return
streams = dataio.data_to_static_streams(das)
# Remove the extension of the filename, to extend the name with .csv
fn_base = dataio.splitext(fn)[0]
ar_streams = [s for s in streams if isinstance(s, ARStream)]
for s in ar_streams:
try:
s.background.value = background
except Exception as ex:
logging.error("Failed to use background data: %s", ex)
ar_proj = stream.ARRawProjection(s)
# Export every position separately
for p in s.point.choices:
if p == (None,
None): # Special "non-selected point" => not interesting
continue
s.point.value = p
# Project to "raw" = Theta vs phi array
exdata = img.ar_to_export_data([ar_proj], raw=True)
# Pick a good name
fn_csv = fn_base
if len(ar_streams) > 1: # Add the name of the stream
fn_csv += "-" + s.name.value
if len(s.point.choices) > 2:
# More than one point in the stream => add position (in µm)
fn_csv += f"-{p[0] * 1e6}-{p[1] * 1e6}"
fn_csv += ".csv"
# Save into a CSV file
logging.info("Exporting point %s to %s", p, fn_csv)
csv.export(fn_csv, exdata)
def testExportSpectrumNoWL(self):
"""Try simple spectrum export"""
size = (10,)
dtype = numpy.uint16
data = model.DataArray(numpy.zeros(size, dtype))
data += 56486
# export
csv.export(FILENAME, data)
# check it's here
st = os.stat(FILENAME) # this test also that the file is created
self.assertGreater(st.st_size, 10)
raised = False
try:
pycsv.reader(open(FILENAME, 'rb'))
except IOError:
raised = True
self.assertFalse(raised, 'Failed to read csv file')
def testExportSpectrumNoWL(self):
"""Try simple spectrum export"""
size = (10, )
dtype = numpy.uint16
md = {model.MD_ACQ_TYPE: model.MD_AT_SPECTRUM, model.MD_DIMS: "C"}
data = model.DataArray(numpy.zeros(size, dtype), md)
data += 56486
# export
csv.export(FILENAME, data)
# check it's here
st = os.stat(FILENAME) # this test also that the file is created
self.assertGreater(st.st_size, 10)
raised = False
try:
pycsv.reader(open(FILENAME, 'rb'))
except IOError:
raised = True
self.assertFalse(raised, 'Failed to read csv file')
def testExportSpectrum(self):
"""Try simple spectrum export"""
size = (150,)
dtype = numpy.uint16
md = {model.MD_WL_LIST: numpy.linspace(536e-9, 650e-9, size[0]).tolist()}
data = model.DataArray(numpy.zeros(size, dtype), md)
data += 56
# export
csv.export(FILENAME, data)
# check it's here
st = os.stat(FILENAME) # this test also that the file is created
self.assertGreater(st.st_size, 150)
raised = False
try:
pycsv.reader(open(FILENAME, 'rb'))
except IOError:
raised = True
self.assertFalse(raised, 'Failed to read csv file')
def testExportSpectrumLineNoWL(self):
"""Try simple spectrum-line export"""
size = (1340, 6)
dtype = numpy.float
md = {model.MD_PIXEL_SIZE: (None, 4.2e-06),
model.MD_ACQ_TYPE: model.MD_AT_SPECTRUM}
data = model.DataArray(numpy.zeros(size, dtype), md)
# export
csv.export(FILENAME, data)
# check it's here
st = os.stat(FILENAME) # this test also that the file is created
self.assertGreater(st.st_size, 5)
raised = False
try:
pycsv.reader(open(FILENAME, 'rb'))
except IOError:
raised = True
self.assertFalse(raised, 'Failed to read csv file')
def testExportAR(self):
"""Try simple AR export"""
size = (90, 360)
dtype = numpy.float
metadata = {
model.MD_DESCRIPTION: "Angle-resolved",
model.MD_ACQ_TYPE: model.MD_AT_AR
}
data = model.DataArray(numpy.zeros(size, dtype), metadata)
data[...] = 26.1561
data[10, 10] = 10
# export
csv.export(FILENAME, data)
# check it's here
st = os.stat(FILENAME) # this test also that the file is created
self.assertGreater(st.st_size, 100)
raised = False
try:
pycsv.reader(open(FILENAME, 'rb'))
except IOError:
raised = True
self.assertFalse(raised, 'Failed to read csv file')
# test intensity value is at correct position
file = pycsv.reader(open(FILENAME, 'r'))
a = numpy.zeros((91, 361))
index = 0
for line in file:
if index == 0:
a[index] = 0.0
else:
a[index] = line
index += 1
# test intensity for same px as defined above is also different when reading back
# (+1 as we add a line for theta/phi MD to the array when exporting)
self.assertEqual(a[11][11], 10)
def testExportAR(self):
"""Try simple AR export"""
size = (101, 401)
dtype = numpy.float
metadata = {model.MD_DESCRIPTION: "Angle-resolved"}
data = model.DataArray(numpy.zeros(size, dtype), metadata)
data += 26.1561
data[1:, 0] = numpy.linspace(0, math.pi / 2, data.shape[0] - 1)
data[0, 1:] = numpy.linspace(0, math.pi * 2, data.shape[1] - 1)
# export
csv.export(FILENAME, data)
# check it's here
st = os.stat(FILENAME) # this test also that the file is created
self.assertGreater(st.st_size, 100)
raised = False
try:
pycsv.reader(open(FILENAME, 'rb'))
except IOError:
raised = True
self.assertFalse(raised, 'Failed to read csv file')
def testExportSpectrumLineNoWL(self):
"""Try simple spectrum-line export"""
size = (1340, 6)
dtype = numpy.float
md = {
model.MD_PIXEL_SIZE: (None, 4.2e-06),
model.MD_ACQ_TYPE: model.MD_AT_SPECTRUM
}
data = model.DataArray(numpy.zeros(size, dtype), md)
# export
csv.export(FILENAME, data)
# check it's here
st = os.stat(FILENAME) # this test also that the file is created
self.assertGreater(st.st_size, 5)
raised = False
try:
pycsv.reader(open(FILENAME, 'rb'))
except IOError:
raised = True
self.assertFalse(raised, 'Failed to read csv file')
def testExportAR(self):
"""Try simple AR export"""
size = (90, 360)
dtype = numpy.float
metadata = {model.MD_DESCRIPTION: "Angle-resolved",
model.MD_ACQ_TYPE: model.MD_AT_AR}
data = model.DataArray(numpy.zeros(size, dtype), metadata)
data[...] = 26.1561
data[10, 10] = 10
# export
csv.export(FILENAME, data)
# check it's here
st = os.stat(FILENAME) # this test also that the file is created
self.assertGreater(st.st_size, 100)
raised = False
try:
pycsv.reader(open(FILENAME, 'rb'))
except IOError:
raised = True
self.assertFalse(raised, 'Failed to read csv file')
# test intensity value is at correct position
file = pycsv.reader(open(FILENAME, 'rb'))
a = numpy.zeros((91, 361))
index = 0
for line in file:
if index == 0:
a[index] = 0.0
else:
a[index] = line
index += 1
# test intensity for same px as defined above is also different when reading back
# (+1 as we add a line for theta/phi MD to the array when exporting)
self.assertEqual(a[11][11], 10)