def test_simple(self):
cyxim = numpy.zeros((3, 512, 256), dtype=numpy.uint8)
cyxim = model.DataArray(cyxim)
orig_shape = cyxim.shape
orig_md = cyxim.metadata.copy()
for i in range(3):
cyxim[i] = i
yxcim = img.ensureYXC(cyxim)
self.assertEqual(yxcim.shape, (512, 256, 3))
self.assertEqual(yxcim.metadata[model.MD_DIMS], "YXC")
# check original da was not changed
self.assertEqual(cyxim.shape, orig_shape)
self.assertDictEqual(orig_md, cyxim.metadata)
# try again with explicit metadata
cyxim.metadata[model.MD_DIMS] = "CYX"
orig_md = cyxim.metadata.copy()
yxcim = img.ensureYXC(cyxim)
self.assertEqual(yxcim.shape, (512, 256, 3))
self.assertEqual(yxcim.metadata[model.MD_DIMS], "YXC")
# check no metadata was changed
self.assertDictEqual(orig_md, cyxim.metadata)
for i in range(3):
self.assertEqual(yxcim[0, 0, i], i)
def _updateImage(self):
""" Recomputes the image with all the raw data available
"""
# logging.debug("Updating image")
if not self.raw:
return
try:
if not isinstance(self.raw, list):
raise AttributeError(".raw must be a list of DA/DAS")
data = self.raw[0]
bkg = self.background.value
if bkg is not None:
try:
data = img.Subtract(data, bkg)
except Exception as ex:
logging.info("Failed to subtract background data: %s", ex)
dims = data.metadata.get(model.MD_DIMS, "CTZYX"[-data.ndim::])
ci = dims.find("C") # -1 if not found
# is RGB
if dims in ("CYX", "YXC") and data.shape[ci] in (3, 4):
rgbim = img.ensureYXC(data)
rgbim.flags.writeable = False
# merge and ensures all the needed metadata is there
rgbim.metadata = self._find_metadata(rgbim.metadata)
rgbim.metadata[model.MD_DIMS] = "YXC" # RGB format
self.image.value = rgbim
else: # is grayscale
if data.ndim != 2:
data = img.ensure2DImage(data) # Remove extra dimensions (of length 1)
self.image.value = self._projectXY2RGB(data, self.tint.value)
except Exception:
logging.exception("Updating %s %s image", self.__class__.__name__, self.name.value)
def new_image(self, data):
"""
Update the window with the new image (the window is resize to have the image
at ratio 1:1)
data (numpy.ndarray): an 2D array containing the image (can be 3D if in RGB)
"""
if data.ndim == 3 and 3 in data.shape: # RGB
rgb = img.ensureYXC(data)
elif numpy.prod(data.shape) == data.shape[-1]: # 1D image => bar plot
# TODO: add "(plot)" to the window title
# Create a simple bar plot of X x 400 px
lenx = data.shape[-1]
leny = 400
maxy = data.max()
logging.info("Plot data max = %s", maxy)
rgb = numpy.zeros((leny, lenx, 3), dtype=numpy.uint8)
for i, v in numpy.ndenumerate(data):
h = leny - int((v * leny) / maxy)
rgb[h:-1, i[-1], :] = 255
else: # Greyscale (hopefully)
mn, mx, mnp, mxp = ndimage.extrema(data)
logging.info("Image data from %s to %s", mn, mx)
rgb = img.DataArray2RGB(data) # auto brightness/contrast
self.app.img = NDImage2wxImage(rgb)
wx.CallAfter(self.app.update_view)
def test_no_change(self):
yxcim = numpy.zeros((512, 256, 3), dtype=numpy.uint8)
yxcim = model.DataArray(yxcim)
yxcim.metadata[model.MD_DIMS] = "YXC"
newim = img.ensureYXC(yxcim)
self.assertEqual(newim.shape, (512, 256, 3))
self.assertEqual(newim.metadata[model.MD_DIMS], "YXC")
def test_find_lens_center(self):
"""
Test FindRingCenter for lenses
"""
data = hdf5.read_data(os.path.join(TEST_IMAGE_PATH, "navcam-calib2.h5"))
imgs = img.RGB2Greyscale(img.ensureYXC(data[0]))
# lens_coordinates = delphi.FindCircleCenter(data[0][0], delphi.LENS_RADIUS, 5)
# expected_coordinates = (-5.9703947e-05, 1.5257675e-04) # (451.5, 445.5) px
lens_coordinates = delphi.FindRingCenter(imgs)
expected_coordinates = (-1.6584835e-05, 1.3084411e-04) # 454.75, 446.1) px
numpy.testing.assert_almost_equal(lens_coordinates, expected_coordinates)
def test_find_lens_center(self):
"""
Test FindRingCenter for lenses
"""
data = hdf5.read_data(os.path.join(TEST_IMAGE_PATH,
"navcam-calib2.h5"))
imgs = img.RGB2Greyscale(img.ensureYXC(data[0]))
# lens_coordinates = delphi.FindCircleCenter(data[0][0], delphi.LENS_RADIUS, 5)
# expected_coordinates = (-5.9703947e-05, 1.5257675e-04) # (451.5, 445.5) px
lens_coordinates = delphi.FindRingCenter(imgs)
expected_coordinates = (-1.6584835e-05, 1.3084411e-04
) # 454.75, 446.1) px
numpy.testing.assert_almost_equal(lens_coordinates,
expected_coordinates)
def new_image(self, data):
"""
Update the window with the new image (the window is resize to have the image
at ratio 1:1)
data (numpy.ndarray): an 2D array containing the image (can be 3D if in RGB)
"""
if data.ndim == 3 and 3 in data.shape: # RGB
rgb = img.ensureYXC(data)
else: # Greyscale (hopefully)
mn, mx, mnp, mxp = ndimage.extrema(data)
logging.info("Image data from %s to %s", mn, mx)
rgb = img.DataArray2RGB(data) # auto brightness/contrast
self.app.img = NDImage2wxImage(rgb)
wx.CallAfter(self.app.update_view)
def _updateImage(self):
# Just pass the RGB data on
if not self.raw:
return
try:
data = self.raw[0]
rgbim = img.ensureYXC(data)
rgbim.flags.writeable = False
# merge and ensures all the needed metadata is there
rgbim.metadata = self._find_metadata(rgbim.metadata)
rgbim.metadata[model.MD_DIMS] = "YXC" # RGB format
self.image.value = rgbim
except Exception:
logging.exception("Updating %s image", self.__class__.__name__)
def _updateImage(self):
# Just pass the RGB data on
if not self.raw:
return
try:
data = self.raw[0]
rgbim = img.ensureYXC(data)
rgbim.flags.writeable = False
# merge and ensures all the needed metadata is there
rgbim.metadata = self._find_metadata(rgbim.metadata)
rgbim.metadata[model.MD_DIMS] = "YXC" # RGB format
self.image.value = rgbim
except Exception:
logging.exception("Updating %s image", self.__class__.__name__)
def _ensureGrayscale(self, data):
''' Ensures that the image is grayscale. If the image is an grayscale RGB,
convert it to an 8bit grayscale image.
data (DataArray or DataArrayShadow): The input image
return (DataArray): The result 8bit grayscale image
raises: ValueError if the image is RGB with different color channels
'''
if len(data.shape) > 3:
raise ValueError("Image format not supported")
elif len(data.shape) == 3:
if isinstance(data, model.DataArrayShadow):
data = data.getData()
data = img.ensureYXC(data)
if (numpy.all(data[:, :, 0] == data[:, :, 1])
and numpy.all(data[:, :, 0] == data[:, :, 2])):
data = data[:, :, 0]
else:
raise ValueError("Coloured RGB image not supported")
return data
def _ensureGrayscale(self, data):
''' Ensures that the image is grayscale. If the image is an grayscale RGB,
convert it to an 8bit grayscale image.
data (DataArray or DataArrayShadow): The input image
return (DataArray): The result 8bit grayscale image
raises: ValueError if the image is RGB with different color channels
'''
if len(data.shape) > 3:
raise ValueError("Image format not supported")
elif len(data.shape) == 3:
if isinstance(data, model.DataArrayShadow):
data = data.getData()
data = img.ensureYXC(data)
if (numpy.all(data[:, :, 0] == data[:, :, 1]) and
numpy.all(data[:, :, 0] == data[:, :, 2])):
data = data[:, :, 0]
else:
raise ValueError("Coloured RGB image not supported")
return data
def _projectTile(self, tile):
"""
Project the tile
tile (DataArray): Raw tile
return (DataArray): Projected tile
"""
dims = tile.metadata.get(model.MD_DIMS, "CTZYX"[-tile.ndim::])
ci = dims.find("C") # -1 if not found
# is RGB
if dims in ("CYX", "YXC") and tile.shape[ci] in (3, 4):
# Just pass the RGB data on
tile = img.ensureYXC(tile)
tile.flags.writeable = False
# merge and ensures all the needed metadata is there
tile.metadata = self.stream._find_metadata(tile.metadata)
tile.metadata[model.MD_DIMS] = "YXC" # RGB format
return tile
else:
if tile.ndim != 2:
tile = img.ensure2DImage(
tile) # Remove extra dimensions (of length 1)
return self._projectXY2RGB(tile, self.stream.tint.value)
def new_image(self, data):
"""
Update the window with the new image (the window is resize to have the image
at ratio 1:1)
data (numpy.ndarray): an 2D array containing the image (can be 3D if in RGB)
"""
if data.ndim == 3 and 3 in data.shape: # RGB
rgb = img.ensureYXC(data)
elif numpy.prod(data.shape) == data.shape[-1]: # 1D image => bar plot
# TODO: add "(plot)" to the window title
# Create a simple bar plot of X x 400 px
lenx = data.shape[-1]
if lenx > MAX_WIDTH:
binning = lenx // MAX_WIDTH
data = data[..., 0::binning]
logging.debug("Compressed data from %d to %d elements", lenx,
data.shape[-1])
lenx = data.shape[-1]
leny = 400
miny = min(0, data.min())
maxy = data.max()
diffy = maxy - miny
if diffy == 0:
diffy = 1
logging.info("Plot data from %s to %s", miny, maxy)
rgb = numpy.zeros((leny, lenx, 3), dtype=numpy.uint8)
for i, v in numpy.ndenumerate(data):
# TODO: have the base at 0, instead of miny, so that negative values are columns going down
h = leny - int(((v - miny) * leny) / diffy)
rgb[h:-1, i[-1], :] = 255
else: # Greyscale (hopefully)
mn, mx, mnp, mxp = ndimage.extrema(data)
logging.info("Image data from %s to %s", mn, mx)
rgb = img.DataArray2RGB(data) # auto brightness/contrast
self.app.spots, self.app.translation, self.app.scaling, self.app.rotation = FindGridSpots(
data, self.gridsize)
self.app.img = NDImage2wxImage(rgb)
wx.CallAfter(self.app.update_view)
def _updateImage(self):
""" Recomputes the image with all the raw data available
"""
# logging.debug("Updating image")
if not self.raw:
return
try:
if not isinstance(self.raw, list):
raise AttributeError(".raw must be a list of DA/DAS")
data = self.raw[0]
bkg = self.background.value
if bkg is not None:
try:
data = img.Subtract(data, bkg)
except Exception as ex:
logging.info("Failed to subtract background data: %s", ex)
dims = data.metadata.get(model.MD_DIMS, "CTZYX"[-data.ndim::])
ci = dims.find("C") # -1 if not found
# is RGB
if dims in ("CYX", "YXC") and data.shape[ci] in (3, 4):
rgbim = img.ensureYXC(data)
rgbim.flags.writeable = False
# merge and ensures all the needed metadata is there
rgbim.metadata = self._find_metadata(rgbim.metadata)
rgbim.metadata[model.MD_DIMS] = "YXC" # RGB format
self.image.value = rgbim
else: # is grayscale
if data.ndim != 2:
data = img.ensure2DImage(
data) # Remove extra dimensions (of length 1)
self.image.value = self._projectXY2RGB(data, self.tint.value)
except Exception:
logging.exception("Updating %s %s image", self.__class__.__name__,
self.name.value)
def _projectTile(self, tile):
"""
Project the tile
tile (DataArray): Raw tile
return (DataArray): Projected tile
"""
dims = tile.metadata.get(model.MD_DIMS, "CTZYX"[-tile.ndim::])
ci = dims.find("C") # -1 if not found
# is RGB
if dims in ("CYX", "YXC") and tile.shape[ci] in (3, 4):
# Just pass the RGB data on
tile = img.ensureYXC(tile)
tile.flags.writeable = False
# merge and ensures all the needed metadata is there
tile.metadata = self.stream._find_metadata(tile.metadata)
tile.metadata[model.MD_DIMS] = "YXC" # RGB format
return tile
elif dims in ("ZYX",) and model.hasVA(self.stream, "zIndex"):
tile = img.getYXFromZYX(tile, self.stream.zIndex.value)
tile.metadata[model.MD_DIMS] = "ZYX"
else:
tile = img.ensure2DImage(tile)
return self._projectXY2RGB(tile, self.stream.tint.value)
def new_image(self, data):
"""
Update the window with the new image (the window is resize to have the image
at ratio 1:1)
data (numpy.ndarray): an 2D array containing the image (can be 3D if in RGB)
"""
if data.ndim == 3 and 3 in data.shape: # RGB
rgb = img.ensureYXC(data)
elif numpy.prod(data.shape) == data.shape[-1]: # 1D image => bar plot
# TODO: add "(plot)" to the window title
# Create a simple bar plot of X x 400 px
lenx = data.shape[-1]
if lenx > MAX_WIDTH:
binning = lenx // MAX_WIDTH
data = data[..., 0::binning]
logging.debug("Compressed data from %d to %d elements", lenx, data.shape[-1])
lenx = data.shape[-1]
leny = 400
miny = min(0, data.min())
maxy = data.max()
diffy = maxy - miny
if diffy == 0:
diffy = 1
logging.info("Plot data from %s to %s", miny, maxy)
rgb = numpy.zeros((leny, lenx, 3), dtype=numpy.uint8)
for i, v in numpy.ndenumerate(data):
# TODO: have the base at 0, instead of miny, so that negative values are columns going down
h = leny - int(((v - miny) * leny) / diffy)
rgb[h:-1, i[-1], :] = 255
else: # Greyscale (hopefully)
mn, mx, mnp, mxp = ndimage.extrema(data)
logging.info("Image data from %s to %s", mn, mx)
rgb = img.DataArray2RGB(data) # auto brightness/contrast
self.app.spots, self.app.translation, self.app.scaling, self.app.rotation = FindGridSpots(data, self.gridsize)
self.app.img = NDImage2wxImage(rgb)
wx.CallAfter(self.app.update_view)
def new_image(self, data):
"""
Update the window with the new image (the window is resize to have the image
at ratio 1:1)
data (numpy.ndarray): an 2D array containing the image (can be 3D if in RGB)
"""
if data.ndim == 3 and 3 in data.shape: # RGB
rgb = img.ensureYXC(data)
elif numpy.prod(data.shape) == 1: # single point => show text
text = "%g" % (data.flat[0], )
logging.info("Data value is: %s", text)
# Create a big enough white space (30x200 px) of BGRA format
rgb = numpy.empty((30, 200, 4), dtype=numpy.uint8)
rgb.fill(255)
# Get a Cairo context for that image
surface = cairo.ImageSurface.create_for_data(
rgb, cairo.FORMAT_ARGB32, rgb.shape[1], rgb.shape[0])
ctx = cairo.Context(surface)
# Draw a black text of 20 px high
ctx.set_source_rgb(0, 0, 0)
ctx.select_font_face("Sans", cairo.FONT_SLANT_NORMAL)
ctx.set_font_size(20)
ctx.move_to(5, 20)
ctx.show_text(text)
del ctx # ensure the context is flushed
elif numpy.prod(data.shape) == data.shape[-1]: # 1D image => bar plot
# TODO: add "(plot)" to the window title
# Create a simple bar plot of X x 400 px
lenx = data.shape[-1]
if lenx > MAX_WIDTH:
binning = lenx // MAX_WIDTH
data = data[..., 0::binning]
logging.debug("Compressed data from %d to %d elements", lenx,
data.shape[-1])
lenx = data.shape[-1]
leny = 400
miny = min(0, data.min())
maxy = data.max()
diffy = maxy - miny
if diffy == 0:
diffy = 1
logging.info("Plot data from %s to %s", miny, maxy)
rgb = numpy.zeros((leny, lenx, 3), dtype=numpy.uint8)
for i, v in numpy.ndenumerate(data):
# TODO: have the base at 0, instead of miny, so that negative values are columns going down
h = leny - int(((v - miny) * leny) / diffy)
rgb[h:-1, i[-1], :] = 255
else: # Greyscale (hopefully)
mn, mx, mnp, mxp = ndimage.extrema(data)
logging.info("Image data from %s to %s", mn, mx)
rgb = img.DataArray2RGB(data) # auto brightness/contrast
self.app.img = NDImage2wxImage(rgb)
disp_size = wx.Display(0).GetGeometry().GetSize()
if disp_size[0] < rgb.shape[1] or disp_size[1] < rgb.shape[0]:
asp_ratio = rgb.shape[1] / rgb.shape[0]
if disp_size[0] / disp_size[1] < asp_ratio:
self.app.magn = disp_size[0] / rgb.shape[1]
else:
self.app.magn = disp_size[1] / rgb.shape[0]
self.app.img.Rescale(rgb.shape[1] * self.app.magn,
rgb.shape[0] * self.app.magn, rgb.shape[2])
else:
self.app.magn = 1
wx.CallAfter(self.app.update_view)
