def setUp(self):
self.app = wx.App()
data = numpy.zeros((2160, 2560), dtype=numpy.uint16)
dataRGB = numpy.zeros((2160, 2560, 4))
metadata = {
'Hardware name': 'Andor ZYLA-5.5-USB3 (s/n: VSC-01959)',
'Exposure time': 0.3,
'Pixel size': (1.59604600574173e-07, 1.59604600574173e-07),
'Acquisition date': 1441361559.258568,
'Hardware version': "firmware: '14.9.16.0' (driver 3.10.30003.5)",
'Centre position': (-0.001203511795256, -0.000295338300158),
'Lens magnification': 40.0,
'Input wavelength range': (6.15e-07, 6.350000000000001e-07),
'Shear': -4.358492733391727e-16,
'Description': 'Filtered colour 1',
'Bits per pixel': 16,
'Binning': (1, 1),
'Pixel readout time': 1e-08,
'Gain': 1.1,
'Rotation': 6.279302551026012,
'Light power': 0.0,
'Display tint': (255, 0, 0),
'Output wavelength range': (6.990000000000001e-07, 7.01e-07)
}
image = model.DataArray(data, metadata)
fluo_stream = stream.StaticFluoStream(metadata['Description'], image)
fluo_stream_pj = stream.RGBSpatialProjection(fluo_stream)
data = numpy.zeros((1024, 1024), dtype=numpy.uint16)
dataRGB = numpy.zeros((1024, 1024, 4))
metadata = {
'Hardware name': 'pcie-6251',
'Description': 'Secondary electrons',
'Exposure time': 3e-06,
'Pixel size': (1e-6, 1e-6),
'Acquisition date': 1441361562.0,
'Hardware version':
'Unknown (driver 2.1-160-g17a59fb (driver ni_pcimio v0.7.76))',
'Centre position': (-0.001203511795256, -0.000295338300158),
'Lens magnification': 5000.0,
'Rotation': 0.0
}
image = model.DataArray(data, metadata)
# export
FILENAME = u"test" + tiff.EXTENSIONS[0]
tiff.export(FILENAME, image, pyramid=True)
# read back
acd = tiff.open_data(FILENAME)
sem_stream = stream.StaticSEMStream(metadata['Description'],
acd.content[0])
sem_stream_pj = stream.RGBSpatialProjection(sem_stream)
sem_stream_pj.mpp.value = 1e-6
self.streams = [fluo_stream_pj, sem_stream_pj]
self.min_res = (623, 432)
# Wait for all the streams to get an RGB image
time.sleep(0.5)
def setUp(self):
self.app = wx.App()
data = numpy.zeros((2160, 2560), dtype=numpy.uint16)
dataRGB = numpy.zeros((2160, 2560, 4))
metadata = {'Hardware name': 'Andor ZYLA-5.5-USB3 (s/n: VSC-01959)',
'Exposure time': 0.3, 'Pixel size': (1.59604600574173e-07, 1.59604600574173e-07),
'Acquisition date': 1441361559.258568, 'Hardware version': "firmware: '14.9.16.0' (driver 3.10.30003.5)",
'Centre position': (-0.001203511795256, -0.000295338300158), 'Lens magnification': 40.0,
'Input wavelength range': (6.15e-07, 6.350000000000001e-07), 'Shear':-4.358492733391727e-16,
'Description': 'Filtered colour 1', 'Bits per pixel': 16, 'Binning': (1, 1), 'Pixel readout time': 1e-08,
'Gain': 1.1, 'Rotation': 6.279302551026012, 'Light power': 0.0, 'Display tint': (255, 0, 0),
'Output wavelength range': (6.990000000000001e-07, 7.01e-07)}
image = model.DataArray(data, metadata)
fluo_stream = stream.StaticFluoStream(metadata['Description'], image)
#fluo_stream.image.value = model.DataArray(dataRGB, metadata)
data = numpy.zeros((1024, 1024), dtype=numpy.uint16)
dataRGB = numpy.zeros((1024, 1024, 4))
metadata = {'Hardware name': 'pcie-6251', 'Description': 'Secondary electrons',
'Exposure time': 3e-06, 'Pixel size': (5.9910982493639e-08, 6.0604642506361e-08),
'Acquisition date': 1441361562.0, 'Hardware version': 'Unknown (driver 2.1-160-g17a59fb (driver ni_pcimio v0.7.76))',
'Centre position': (-0.001203511795256, -0.000295338300158), 'Lens magnification': 5000.0, 'Rotation': 0.0,
'Shear': 0.003274715695854}
image = model.DataArray(data, metadata)
sem_stream = stream.StaticSEMStream(metadata['Description'], image)
#sem_stream.image.value = model.DataArray(dataRGB, metadata)
# create DataProjections for the streams
fluo_stream_pj = stream.RGBSpatialProjection(fluo_stream)
sem_stream_pj = stream.RGBSpatialProjection(sem_stream)
self.streams = [fluo_stream_pj, sem_stream_pj]
self.min_res = (623, 432)
# Spectrum stream
data = numpy.ones((251, 1, 1, 200, 300), dtype="uint16")
data[:, 0, 0, :, 3] = range(200)
data[:, 0, 0, :, 3] *= 3
data[:, 0, 0, 1, 3] = range(251)
data[2, :, :, :, :] = range(300)
data[200, 0, 0, 2] = range(300)
wld = 433e-9 + numpy.array(range(data.shape[0])) * 0.1e-9
md = {model.MD_SW_VERSION: "1.0-test",
model.MD_HW_NAME: "fake ccd",
model.MD_DESCRIPTION: "Spectrum",
model.MD_ACQ_DATE: time.time(),
model.MD_BPP: 12,
model.MD_PIXEL_SIZE: (2e-6, 2e-6), # m/px
model.MD_POS: (-0.001203511795256, -0.000295338300158), # m
model.MD_EXP_TIME: 0.2, # s
model.MD_LENS_MAG: 60, # ratio
model.MD_WL_LIST: wld,
}
spec_data = model.DataArray(data, md)
self.spec_stream = stream.StaticSpectrumStream("test spec", spec_data)
# Wait for all the streams to get an RGB image
time.sleep(0.5)
def _openImage(self, filename, tint, shiftX, shiftY):
""" Open the given filename and assign the tint of the corresponding channel. Add the stream to the dialog and
apply the crop functionality. Two sliders are displayed for every image to provide the option of shifting the
streams in x and y dimension. If there is no filename given return None.
Args:
filename(str) : the given filename with the R, G or B stream
tint(tuple): the color tint to be assigned
shiftX(ContinuousVA): shift x value in meters
shiftY(ContinuousVA): shift y value in meters
Returns (Stream or None): the displayed stream
"""
if filename == " ":
return None
try:
data = udataio.open_acquisition(filename)[0]
pxs = data.metadata.get(model.MD_PIXEL_SIZE, (1e-06, 1e-06))
if pxs[0] > 1e-04 or pxs[1] > 1e-04:
data.metadata[model.MD_PIXEL_SIZE] = (1e-06, 1e-06)
logging.warning(
"The given pixel size %s is too big, it got replaced to the default value %s",
pxs, (1e-06, 1e-06))
data = self._ensureRGB(data, tint)
except Exception as ex:
logging.exception("Failed to open %s", filename)
self._showErrorMessage("Failed to open image",
"Failed to open image:\n%s" % (ex, ))
return None
basename, ext = os.path.splitext(os.path.split(filename)[1])
stream_ch = stream.StaticFluoStream(basename, data)
self._raw_orig[stream_ch] = data
self._dlg.addStream(stream_ch)
self._setupStreambar()
self._cropBottom()
self._connectShift(stream_ch, 0, shiftX)
self._connectShift(stream_ch, 1, shiftY)
return stream_ch