def test_load_simple(self):
# AR background data
dcalib = numpy.zeros((512, 1024), dtype=numpy.uint16)
md = {
model.MD_SW_VERSION: "1.0-test",
model.MD_HW_NAME: "fake ccd",
model.MD_DESCRIPTION: "AR",
model.MD_ACQ_DATE: time.time(),
model.MD_BPP: 12,
model.MD_BINNING: (1, 1), # px, px
model.MD_SENSOR_PIXEL_SIZE: (13e-6, 13e-6), # m/px
model.MD_PIXEL_SIZE: (1e-6, 2e-5), # m/px
model.MD_POS: (1.2e-3, -30e-3), # m
model.MD_EXP_TIME: 1.2, # s
model.MD_AR_POLE: (253.1, 65.1),
model.MD_LENS_MAG: 60, # ratio
}
calib = model.DataArray(dcalib, md)
# Give one DA, the correct one, so expect to get it back
out = calibration.get_ar_data([calib])
numpy.testing.assert_equal(out, calib)
# More DataArrays, just to make it slightly harder to find the data
data1 = model.DataArray(numpy.ones((1, 1, 1, 520, 230),
dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
data2 = model.DataArray(17 * numpy.ones((1, 1), dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
out = calibration.get_ar_data([data1, calib, data2])
numpy.testing.assert_equal(out, calib)
def test_load_simple(self):
# AR background data
dcalib = numpy.zeros((512, 1024), dtype=numpy.uint16)
md = {model.MD_SW_VERSION: "1.0-test",
model.MD_HW_NAME: "fake ccd",
model.MD_DESCRIPTION: "AR",
model.MD_ACQ_DATE: time.time(),
model.MD_BPP: 12,
model.MD_BINNING: (1, 1), # px, px
model.MD_SENSOR_PIXEL_SIZE: (13e-6, 13e-6), # m/px
model.MD_PIXEL_SIZE: (1e-6, 2e-5), # m/px
model.MD_POS: (1.2e-3, -30e-3), # m
model.MD_EXP_TIME: 1.2, # s
model.MD_AR_POLE: (253.1, 65.1),
model.MD_LENS_MAG: 60, # ratio
}
calib = model.DataArray(dcalib, md)
# Give one DA, the correct one, so expect to get it back
out = calibration.get_ar_data([calib])
numpy.testing.assert_equal(out, calib)
# More DataArrays, just to make it slightly harder to find the data
data1 = model.DataArray(numpy.ones((1, 1, 1, 520, 230), dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
data2 = model.DataArray(17 * numpy.ones((1, 1), dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
out = calibration.get_ar_data([data1, calib, data2])
numpy.testing.assert_equal(out, calib)
def test_load_simple_arpol(self):
# AR polarimetry background data
metadata = []
pol_positions = list(POL_POSITIONS)
qwp_positions = [0.0, 1.570796, 0.785398, 2.356194, 0.0, 0.0]
linpol_positions = [
0.0, 1.570796, 0.785398, 2.356194, 0.785398, 2.356194
]
# ARPOL metadata
for idx in range(len(pol_positions)):
metadata.append({
model.MD_SW_VERSION: "1.0-test",
model.MD_HW_NAME: "fake ccd",
model.MD_DESCRIPTION: "ARPOL",
model.MD_ACQ_DATE: time.time(),
model.MD_BPP: 12,
model.MD_BINNING: (1, 1), # px, px
model.MD_SENSOR_PIXEL_SIZE: (13e-6, 13e-6), # m/px
model.MD_PIXEL_SIZE: (2e-5, 2e-5), # m/px
model.MD_POS: (1.2e-3, -30e-3), # m
model.MD_EXP_TIME: 1.2, # s
model.MD_AR_POLE: (253.1, 65.1),
model.MD_LENS_MAG: 0.4, # ratio
model.MD_POL_MODE: pol_positions[idx],
model.MD_POL_POS_LINPOL: qwp_positions[idx], # rad
model.MD_POL_POS_QWP: linpol_positions[idx], # rad
})
bg_data = [] # list of background images
for idx in range(len(pol_positions)):
dcalib = numpy.ones(
(1, 1, 1, 512, 1024),
dtype=numpy.uint16) + idx # different bg image for each pol
calib = model.DataArray(dcalib, metadata[idx])
bg_data.append(calib)
# Give one DA, the correct one, so expect to get it back
out = calibration.get_ar_data(bg_data)
# Check the expected and return lists contain the same DataArrays
self.assertEqual(len(bg_data), len(out))
for da in out:
self.assertTrue(any(numpy.array_equal(da, bg) for bg in bg_data))
# More DataArrays, just to make it slightly harder to find the data
data1 = model.DataArray(numpy.ones((1, 1, 1, 520, 230),
dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
data2 = model.DataArray(17 * numpy.ones((1, 1), dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
bg_data_new = [data1, data2] + bg_data
out = calibration.get_ar_data(bg_data_new)
# Check the expected and return lists contain the same DataArrays
self.assertEqual(len(bg_data), len(out))
for da in out:
self.assertTrue(any(numpy.array_equal(da, bg) for bg in bg_data))
def test_load_full(self):
"""
Check the whole sequence: saving calibration data to file, loading it
back from file, finding it.
"""
# AR background data
dcalib = numpy.zeros((512, 1024), dtype=numpy.uint16)
md = {
model.MD_SW_VERSION: "1.0-test",
model.MD_HW_NAME: "fake ccd",
model.MD_DESCRIPTION: "AR",
model.MD_ACQ_DATE: time.time(),
model.MD_BPP: 12,
model.MD_BINNING: (1, 1), # px, px
model.MD_SENSOR_PIXEL_SIZE: (13e-6, 13e-6), # m/px
model.MD_PIXEL_SIZE: (1e-6, 2e-5), # m/px
model.MD_POS: (1.2e-3, -30e-3), # m
model.MD_EXP_TIME: 1.2, # s
model.MD_AR_POLE: (253.1, 65.1),
model.MD_LENS_MAG: 60, # ratio
}
calib = model.DataArray(dcalib, md)
# Give one DA, the correct one, so expect to get it back
out = calibration.get_ar_data([calib])
numpy.testing.assert_equal(out, calib)
# More DataArrays, just to make it slightly harder to find the data
data1 = model.DataArray(numpy.ones((1, 1, 1, 520, 230),
dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
data2 = model.DataArray(17 * numpy.ones((1, 1), dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
# RGB image
thumb = model.DataArray(numpy.ones((520, 230, 3), dtype=numpy.uint8))
full_data = [data1, calib, data2]
for fmt in dataio.get_available_formats(os.O_WRONLY):
exporter = dataio.get_converter(fmt)
logging.info("Trying to export/import with %s", fmt)
fn = u"test_ar" + exporter.EXTENSIONS[0]
exporter.export(fn, full_data, thumb)
if fmt in dataio.get_available_formats(os.O_RDONLY):
idata = exporter.read_data(fn)
icalib = calibration.get_ar_data(idata)
icalib2d = img.ensure2DImage(icalib)
numpy.testing.assert_equal(icalib2d, calib)
numpy.testing.assert_almost_equal(
icalib.metadata[model.MD_AR_POLE],
calib.metadata[model.MD_AR_POLE])
try:
os.remove(fn)
except OSError:
logging.exception("Failed to delete the file %s", fn)
def test_load_full(self):
"""
Check the whole sequence: saving calibration data to file, loading it
back from file, finding it.
"""
# AR background data
dcalib = numpy.zeros((512, 1024), dtype=numpy.uint16)
md = {model.MD_SW_VERSION: "1.0-test",
model.MD_HW_NAME: "fake ccd",
model.MD_DESCRIPTION: "AR",
model.MD_ACQ_DATE: time.time(),
model.MD_BPP: 12,
model.MD_BINNING: (1, 1), # px, px
model.MD_SENSOR_PIXEL_SIZE: (13e-6, 13e-6), # m/px
model.MD_PIXEL_SIZE: (1e-6, 2e-5), # m/px
model.MD_POS: (1.2e-3, -30e-3), # m
model.MD_EXP_TIME: 1.2, # s
model.MD_AR_POLE: (253.1, 65.1),
model.MD_LENS_MAG: 60, # ratio
}
calib = model.DataArray(dcalib, md)
# Give one DA, the correct one, so expect to get it back
out = calibration.get_ar_data([calib])
numpy.testing.assert_equal(out, calib)
# More DataArrays, just to make it slightly harder to find the data
data1 = model.DataArray(numpy.ones((1, 1, 1, 520, 230), dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
data2 = model.DataArray(17 * numpy.ones((1, 1), dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
# RGB image
thumb = model.DataArray(numpy.ones((520, 230, 3), dtype=numpy.uint8))
full_data = [data1, calib, data2]
for fmt in dataio.get_available_formats(os.O_WRONLY):
exporter = dataio.get_converter(fmt)
logging.info("Trying to export/import with %s", fmt)
fn = u"test_ar" + exporter.EXTENSIONS[0]
exporter.export(fn, full_data, thumb)
if fmt in dataio.get_available_formats(os.O_RDONLY):
idata = exporter.read_data(fn)
icalib = calibration.get_ar_data(idata)
icalib2d = img.ensure2DImage(icalib)
numpy.testing.assert_equal(icalib2d, calib)
numpy.testing.assert_almost_equal(icalib.metadata[model.MD_AR_POLE],
calib.metadata[model.MD_AR_POLE])
try:
os.remove(fn)
except OSError:
logging.exception("Failed to delete the file %s", fn)
def test_load_simple_arpol(self):
# AR polarimetry background data
metadata = []
pol_positions = list(POL_POSITIONS)
qwp_positions = [0.0, 1.570796, 0.785398, 2.356194, 0.0, 0.0]
linpol_positions = [0.0, 1.570796, 0.785398, 2.356194, 0.785398, 2.356194]
# ARPOL metadata
for idx in range(len(pol_positions)):
metadata.append({model.MD_SW_VERSION: "1.0-test",
model.MD_HW_NAME: "fake ccd",
model.MD_DESCRIPTION: "ARPOL",
model.MD_ACQ_DATE: time.time(),
model.MD_BPP: 12,
model.MD_BINNING: (1, 1), # px, px
model.MD_SENSOR_PIXEL_SIZE: (13e-6, 13e-6), # m/px
model.MD_PIXEL_SIZE: (2e-5, 2e-5), # m/px
model.MD_POS: (1.2e-3, -30e-3), # m
model.MD_EXP_TIME: 1.2, # s
model.MD_AR_POLE: (253.1, 65.1),
model.MD_LENS_MAG: 0.4, # ratio
model.MD_POL_MODE: pol_positions[idx],
model.MD_POL_POS_LINPOL: qwp_positions[idx], # rad
model.MD_POL_POS_QWP: linpol_positions[idx], # rad
})
bg_data = [] # list of background images
for idx in range(len(pol_positions)):
dcalib = numpy.ones((1, 1, 1, 512, 1024), dtype=numpy.uint16) + idx # different bg image for each pol
calib = model.DataArray(dcalib, metadata[idx])
bg_data.append(calib)
# Give one DA, the correct one, so expect to get it back
out = calibration.get_ar_data(bg_data)
numpy.testing.assert_equal(out, bg_data) # all bg images should have same shape
# More DataArrays, just to make it slightly harder to find the data
data1 = model.DataArray(numpy.ones((1, 1, 1, 520, 230), dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
data2 = model.DataArray(17 * numpy.ones((1, 1), dtype=numpy.uint16),
metadata={model.MD_POS: (1.2e-3, -30e-3)})
bg_data_new = [data1, data2] + bg_data
out = calibration.get_ar_data(bg_data_new)
numpy.testing.assert_equal(out, bg_data)
def main(args):
"""
Handles the command line arguments
args is the list of arguments passed
return (int): value to return to the OS as program exit code
"""
# arguments handling
parser = argparse.ArgumentParser(
description="Batch export of AR data to CSV")
parser.add_argument("--background",
"-b",
dest="background",
help="Name of background data")
parser.add_argument(dest="filenames",
nargs="+",
help="List of (HDF5) files containing the AR data")
options = parser.parse_args(args[1:])
try:
if options.background:
data = dataio.open_acquisition(options.background)
if not data:
return 1
# will raise exception if doesn't contain good calib data
bkg = calibration.get_ar_data(data)
else:
bkg = None
if os.name == 'nt':
# on Windows, the application is in charge of expanding "*".
filenames = []
for fn in options.filenames:
filenames.extend(glob.glob(fn))
else:
filenames = options.filenames
for fn in filenames:
export_ar_to_csv(fn, bkg)
except:
logging.exception("Unexpected error while performing action.")
return 127
return 0