now there is an image processing to compute the radial profile (needed for graffy/lipase#3).
This commit is contained in:
Guillaume Raffy
parent
e8b1e331fe
commit
4daf2bfe91
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@ -0,0 +1,123 @@
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"""
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an image processing technique to produce a 1D signal for each pixel : this 1D signal is obtained by projecting the neighborhood of this pixel on a set of bases (each base is used as a convilution kernel)
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https://subversion.ipr.univ-rennes1.fr/repos/main/projects/antipode/src/python/antipode/texori.py
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"""
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from imageengine import IImageEngine, PixelType
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class IProjectorBase(object):
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"""
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a set of projectors
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a projector is a grey level image, in which each pixel value is acting as a weight
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"""
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def __init__(self):
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pass
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def get_num_projectors(self):
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pass
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def get_projector_kernel(self, projector_index):
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pass
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def create_circle_image(image_size, circle_radius, circle_pos, circle_thickness, background_value=0.0, circle_value=1.0):
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"""
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:param dict image_size:
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"""
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ie = IImageEngine.get_instance()
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width = image_size['width']
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height = image_size['height']
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assert isinstance(width, int)
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assert isinstance(height, int)
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circle_pos_x = float(circle_pos['x'])
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circle_pos_y = float(circle_pos['y'])
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r_min = max(0.0, circle_radius - circle_thickness * 0.5)
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r_max = circle_radius + circle_thickness * 0.5
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r_min_square = r_min * r_min
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r_max_square = r_max * r_max
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image = ie.create_image(width=width, height=height, pixel_type=PixelType.F32)
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for y in range(height):
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for x in range(width):
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dx = x - circle_pos_x
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dy = y - circle_pos_y
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r_square = (dx * dx + dy * dy)
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if r_min_square < r_square < r_max_square:
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pixel_value = circle_value
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else:
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pixel_value = background_value
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image.set_pixel(x, y, pixel_value)
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return image
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class CircularSymmetryProjectorBase(IProjectorBase):
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"""
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generates a base of circles
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"""
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def __init__(self, max_radius, oversampling_scale=2):
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"""
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:param int max_radius: the biggest circle radius in the set of projectors
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:param int oversampling_scale: oversampling is used to generate antialased circles. The higher this value, the better the quality of antialiasing is
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"""
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super(CircularSymmetryProjectorBase, self).__init__()
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assert max_radius > 0
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assert oversampling_scale > 0
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self.max_radius = max_radius
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self.oversampling_scale = oversampling_scale
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self.num_projectors = int(max_radius) + 1
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def get_num_projectors(self):
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return self.num_projectors
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def get_projector_kernel(self, projector_index):
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assert projector_index < self.get_num_projectors()
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oversampling_is_handled = False # TODO: handle oversampling to increase quality
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if not oversampling_is_handled and self.oversampling_scale != 1 :
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raise NotImplementedError("at the moment, oversampling is not yet implemented")
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radius = projector_index
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image_size = int(self.max_radius) * 2 + 1
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circle_pos = {'x': self.max_radius, 'y': self.max_radius}
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oversampled_circle = create_circle_image(
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image_size={'width': image_size * self.oversampling_scale, 'height': image_size*self.oversampling_scale},
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circle_radius=radius * self.oversampling_scale,
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circle_pos={'x': self.max_radius* self.oversampling_scale, 'y': self.max_radius* self.oversampling_scale},
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circle_thickness=1 * self.oversampling_scale)
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if self.oversampling_scale == 1:
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circle_image = oversampled_circle
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else:
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if oversampling_is_handled:
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circle_image = oversampled_circle.resample(width=image_size, height=image_size)
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# mean_value = circle_image.get_mean_value()
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# num_pixels = image_size * image_size
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# sum_of_pixel_values = mean_value * num_pixels
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# we want each circle to have a total weight of 1.0, regardless their radius
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# circle_image.scale_values(1.0/sum_of_pixel_values)
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anchor_point = {'x': int(circle_pos['x']), 'y': int(circle_pos['y'])}
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return circle_image, anchor_point
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class CircularSymmetryDetector:
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def __init__(self, max_radius):
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"""
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:para float max_radius:
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"""
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self.max_radius = max_radius
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def compute_radial_profiles(self, src_image):
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""" Computes for each pixel the radial profile (with this pixel as center)
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:param IImage src_image:
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:rtype IHyperstack: each radial profile is stored in the channel coordinate of the hyperstack
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"""
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ie = IImageEngine.get_instance()
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ie.debugger.on_image(src_image, 'src_image')
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projector_base = CircularSymmetryProjectorBase(self.max_radius, oversampling_scale=1)
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radial_profile_image = ie.create_hyperstack(width=src_image.get_width(), height=src_image.get_height(), num_channels=projector_base.get_num_projectors(), num_slices=1, num_frames=1, pixel_type=PixelType.F32)
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for projector_index in range(projector_base.get_num_projectors()):
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projector, center_of_filter = projector_base.get_projector_kernel(projector_index)
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ie.debugger.on_image(projector, 'projector_%d' % (projector_index))
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print(type(center_of_filter))
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projection = ie.filter2D(src_image, dst_type=PixelType.F32, kernel=projector, anchor=(center_of_filter['x'], center_of_filter['y']))
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ie.debugger.on_image(projection, 'projection_%d' % (projector_index))
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radial_profile_image.set_image(self, projection, frame_index=0, slice_index=0, channel_index=projector_index)
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return radial_profile_image
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@ -97,6 +97,14 @@ class IImage(ABC):
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"""
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pass
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@abc.abstractmethod
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def scale_values(self, src_image, scale):
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"""
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multiply the value of each pixel by a the given scalar
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:param float scale:
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"""
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class IHyperStack(ABC):
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@abc.abstractmethod
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@ -426,6 +434,17 @@ class IImageEngine(ABC):
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:param int radius: in pixels
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"""
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@abc.abstractmethod
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def filter2D(self, src_image, dst_type, kernel, anchor=(-1, -1)):
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""" as cv2.filter2D
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:param IImage src_image:
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:param PixelType or None dst_type: pixel type of the destination image (if None, the pixel type is the same as the source image type)
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:param IImage kernel: convolution kernel (or rather a correlation kernel), a single-channel floating point matrix; if you want to apply different kernels to different channels, split the image into separate color planes using split() and process them individually.
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:param tuple(int, int) angor: anchor of the kernel that indicates the relative position of a filtered point within the kernel; the anchor should lie within the kernel; default value (-1,-1) means that the anchor is at the kernel center.
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:rtype IImage:
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"""
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@abc.abstractmethod
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def perform_gray_morphology(self, image, operator, structuring_element_shape, structuring_element_radius):
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"""
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@ -515,3 +534,4 @@ class IImageEngine(ABC):
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:param IImage src_binary_image:
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:rtype IImage: binary image
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"""
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@ -24,6 +24,12 @@ IJ_PIXELTYPE_TO_PIXEL_TYPE = {
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ImagePlus.GRAY32: PixelType.F32
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}
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PIXEL_TYPE_TO_CV_PIXEL_TYPE = {
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PixelType.U8: opencv_core.CV_8U,
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PixelType.U16: opencv_core.CV_16U,
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PixelType.F32: opencv_core.CV_32F,
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}
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class IJImage(IImage):
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def __init__(self, image_engine, ij_image=None, width=None, height=None, pixel_type=None):
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@ -101,6 +107,10 @@ class IJImage(IImage):
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image_stats = processor.getStats() # :type ImageStatistics image_stats:
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return image_stats.mean
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def scale_values(self, scale):
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raise NotImplementedError()
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class IJHyperStack(IHyperStack):
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def __init__(self, image_engine, width, height, num_channels, num_slices, num_frames, pixel_type):
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@ -231,6 +241,7 @@ def perform_gray_morphology_with_ijopencv(image, operator, structuring_element_s
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mat2imp = MatImagePlusConverter()
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image.ij_image.setProcessor(mat2imp.toImageProcessor(cv_dst_image))
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class ImageLogger(IImageProcessingDebugger):
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def __init__(self):
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"""Implement interface method."""
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IJ.run(image.ij_image, "Mean...", "radius=%d" % radius)
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def filter2D(self, src_image, dst_type, kernel, anchor=(-1, -1)):
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print(type(anchor), anchor)
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if anchor == (-1, -1):
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assert kernel.get_width() % 2 == 1 and kernel.get_height() % 2 == 1, "kernel sizes are expected to be odd if you want the anchor to be at the center of the kernel"
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anchor = ((kernel.get_width() - 1) / 2, (kernel.get_height() - 1) / 2)
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imp2mat = ImagePlusMatConverter()
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cv_src_image = imp2mat.toMat(src_image.ij_image.getProcessor())
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cv_kernel = imp2mat.toMat(kernel.ij_image.getProcessor())
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cv_anchor = opencv_core.Point(anchor[0], anchor[1])
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ie = IImageEngine.get_instance()
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dst_image = ie.create_image(width=src_image.get_width(), height=src_image.get_height(), pixel_type=PixelType.F32)
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cv_dst_image = opencv_core.Mat(cv_src_image.size(), cv_src_image.type())
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# warning ! trying to guess the arguments from opencv's documentation is time consuming as the error messages are misleading (in the following call, javacpp complains that the 1st argument is not a org.bytedeco.javacpp.opencv_core$Mat, while it is ! The problem comes from the order of the arguments). So, instead of guessing, the found accepted signatures of filter2D are in https://github.com/bytedeco/javacpp-presets/blob/master/opencv/src/gen/java/org/bytedeco/opencv/global/opencv_imgproc.java
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# opencv_imgproc.morphologyEx(cv_src_image, opencv_imgproc.MORPH_OPEN, struct_element, dst_image)
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# TypeError: morphologyEx(): 1st arg can't be coerced to org.bytedeco.javacpp.opencv_core$GpuMat, org.bytedeco.javacpp.opencv_core$Mat, org.bytedeco.javacpp.opencv_core$UMat
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print('before opencv_imgproc.filter2D')
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delta = 0
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border_type = opencv_core.BORDER_DEFAULT
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if dst_type is None:
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ddepth = -1
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else:
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ddepth = PIXEL_TYPE_TO_CV_PIXEL_TYPE[dst_type]
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opencv_imgproc.filter2D(cv_src_image, cv_dst_image, ddepth, cv_kernel, cv_anchor, delta, border_type)
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print('after opencv_imgproc.filter2D')
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mat2imp = MatImagePlusConverter()
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dst_image.ij_image.setProcessor(mat2imp.toImageProcessor(cv_dst_image))
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return dst_image
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def perform_gray_morphology(self, image, operator, structuring_element_shape, structuring_element_radius):
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"""
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:param IJImage image:
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@ -1,143 +0,0 @@
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"""
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an image processing technique to produce a 1D signal for each pixel : this 1D signal is obtained by projecting the neighborhood of this pixel on a set of bases (each base is used as a convilution kernel)
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https://subversion.ipr.univ-rennes1.fr/repos/main/projects/antipode/src/python/antipode/texori.py
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"""
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from imageengine import IImageEngine, PixelType
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class IProjectorBase(object):
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"""
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a set of projectors
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a projector is a grey level image, in which each pixel value is acting as a weight
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"""
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def __init__(self):
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pass
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def get_num_projectors(self):
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pass
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def get_projector_kernel(self, projector_index):
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pass
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def create_circle_image(image_size, circle_radius, circle_pos, circle_thickness, background_value=0.0, circle_value=1.0):
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"""
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:param dict image_size:
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"""
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ie = IImageEngine.get_instance()
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width = image_size['width']
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height = image_size['height']
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circle_pos_x = float(circle_pos['x'])
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circle_pos_y = float(circle_pos['y'])
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r_min = circle_radius - circle_thickness * 0.5
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assert r_min >= 0.0
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r_max = circle_radius + circle_thickness * 0.5
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r_min_square = r_min * r_min
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r_max_square = r_max * r_max
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image = ie.create_image(width=width, height=height, pixel_type=PixelType.F32)
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for y in range(height):
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for x in range(width):
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dx = x - circle_pos_x
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dy = y - circle_pos_y
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r_square = (dx * dx + dy * dy)
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if r_min_square < r_square < r_max_square:
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pixel_value = circle_value
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else:
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pixel_value = background_value
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image.set_pixel(x, y, pixel_value)
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return image
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class CircularSymetryProjectorBase(IProjectorBase):
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"""
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generates a base of circles
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"""
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def __init__(self, max_radius, oversampling_scale=2):
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"""
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:param int max_radius: the biggest circle radius in the set of projectors
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:param int oversampling_scale: oversampling is used to generate antialased circles. The higher this value, the better the quality of antialiasing is
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"""
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super().__init__()
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assert max_radius > 0
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assert oversampling_scale > 0
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self.max_radius = max_radius
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self.oversampling_scale = oversampling_scale
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self.num_projectors = max_radius + 1
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def get_num_projectors(self):
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return self.num_projectors
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def get_projector_kernel(self, projector_index):
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assert projector_index < self.get_num_projectors()
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radius = projector_index
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image_size = self.max_radius * 2 + 1
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circle_pos = {'x': self.max_radius, 'y': self.max_radius}
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oversampled_circle = create_circle_image(
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image_size={'width':image_size * self.oversampling_scale, 'height':image_size*self.oversampling_scale},
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circle_radius=radius * self.oversampling_scale,
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circle_pos={'x': self.max_radius* self.oversampling_scale, 'y': self.max_radius* self.oversampling_scale},
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circle_thickness=1 * self.oversampling_scale)
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circle_image = oversampled_circle.resample(width=image_size, height=image_size)
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anchor_point = circle_pos
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return circle_image, anchor_point
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# class LocalProjector:
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# """ This image processor computes the probability for each pixel to have a material oriented in the given direction
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# The technique is based on the notion of a projector. The role of the projector is to project (or cumulate) the 2D neighborhood of each pixel on a projection axis that passes through the pixel and that has an orientation chosen by the user.
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# """
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# def __init__(self, searched_orientation, image_process_listener=imageprocessing.NullImageProcessListener()):
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# imageprocessing.IImageProcessor.__init__(self, image_process_listener)
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# self.searched_orientation = searched_orientation
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# self.orientation_amount_image = None
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# @staticmethod
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# def compute_noise_in_perpendicular_orientation(src_image, orientation, half_window_width=5, image_process_listener=imageprocessing.NullImageProcessListener()):
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# """ Computes an image that gives for each pixel, the amount of noise in a direction perpendicular to the given orientation
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# Because the projection has to be performed for each pixel, we encode the projector operator in the form of a set of num_projectors 2D kernels that are used as a filter. Each kernel cumulates the image signal (therefore computes the sum of the image signal) along a line perpendicular to the projection axis, but each at a different position (offset) on this projection axis.
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# :param src_image: the input image, the one we want to process
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# :type src_image: numpy.array
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# :param orientation: the orientation along which the noise needs to be computed
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# :type orientation: float (in radians)
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# :param half_window_width: half size of the neighborhood window, in pixels (the heighborood window is a window of size (2*half_window_width+1, 2*half_window_width+1) centered on each pixel). The bigger, the more precise the measurement but with less locality.
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# """
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# projector_base = OrientationProbabilityEstimator.ProjectorBase2(orientation, searched_segment_size=10.0, cut_blur_stddev=3.0, image_process_listener=image_process_listener)
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# projections = numpy.empty((src_image.shape[0], src_image.shape[1], projector_base.get_num_projectors()), dtype=numpy.float32)
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# # print('projections.shape=%s' % str(projections.shape))
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# for projector_index in range(projector_base.get_num_projectors()):
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# projector, center_of_filter = projector_base.get_projector_kernel(projector_index)
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# projection = cv2.filter2D(src_image.astype(numpy.float32), ddepth=-1, kernel=projector, anchor=tuple(center_of_filter))
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# image_process_listener.onImage(projection, 'projection_%f_%d' % (orientation, projector_index))
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# projections[:, :, projector_index] = projection
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# # for each pixel, compute the gradient along its projection axis
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# # swap axes because I don't think the filter2D only works along fist 2 axes
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# projections = numpy.swapaxes(projections, 1, 2)
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# grad_kernel = numpy.array((-0.5, 0.5), dtype=numpy.float32)
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# gradients = cv2.filter2D(projections, ddepth=-1, kernel=grad_kernel, anchor=(0, 0))
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# if image_process_listener is not None:
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# # grab a slice of the gradient image for debugging purpose
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# cut = gradients[:, :, gradients.shape[2] / 2]
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# image_process_listener.onImage(cut, 'cut_%f' % (orientation))
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# gradients = numpy.swapaxes(gradients, 1, 2)
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# gradients *= gradients
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# texture_amount = numpy.sum(gradients, axis=2)
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# image_process_listener.onImage(texture_amount, 'texture_amount_%f' % (orientation))
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# return texture_amount
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# def processImage(self, image):
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# self.orientation_amount_image = OrientationProbabilityEstimator.compute_noise_in_perpendicular_orientation(image, self.searched_orientation, self.get_image_process_listener())
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# def get_result(self):
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# return self.orientation_amount_image
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@ -8,7 +8,7 @@ import unittest # unittest2 doesn't exist in fiji
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import sys
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from lipase.imageengine import IImageEngine, PixelType, Aabb, NullDebugger, FileBasedDebugger
|
||||
from lipase.imagej.ijimageengine import IJImageEngine, IJImage
|
||||
from lipase.localprojector import create_circle_image
|
||||
from lipase.circsymdetector import create_circle_image
|
||||
|
||||
class ImProcTester(unittest.TestCase):
|
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|
||||
|
|
|
|||
|
|
@ -16,6 +16,7 @@ from lipase.traps_detector import TrapsDetector
|
|||
from lipase.catalog import ImageCatalog, Sequence
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||||
from lipase.lipase import Lipase, ImageLogger
|
||||
from lipase.lipase import GlobulesAreaEstimator, EmptyFrameBackgroundEstimator
|
||||
from lipase.circsymdetector import CircularSymmetryDetector
|
||||
from lipase.imagej.hdf5serializer import save_hdf5_file
|
||||
|
||||
|
||||
|
|
@ -35,78 +36,86 @@ class TestLipase(unittest.TestCase):
|
|||
print("uninitializing TestLipase instance")
|
||||
self.catalog = None
|
||||
|
||||
def test_estimate_white(self):
|
||||
sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']
|
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white_estimator = WhiteEstimator(open_size=75, close_size=75, average_size=75)
|
||||
white_estimate = white_estimator.estimate_white([sequence], ['DM300_327-353_fluo'])
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||||
# find_white_reference_image(white_estimate, sequence.get_white())
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print(white_estimate)
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IImageEngine.get_instance().debugger.on_image(white_estimate, 'white_estimate')
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||||
# assert False, "hellooooo"
|
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print('end of test_estimate_white')
|
||||
# def test_estimate_white(self):
|
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# sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']
|
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# white_estimator = WhiteEstimator(open_size=75, close_size=75, average_size=75)
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||||
# white_estimate = white_estimator.estimate_white([sequence], ['DM300_327-353_fluo'])
|
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# # find_white_reference_image(white_estimate, sequence.get_white())
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# print(white_estimate)
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||||
# IImageEngine.get_instance().debugger.on_image(white_estimate, 'white_estimate')
|
||||
# # assert False, "hellooooo"
|
||||
# print('end of test_estimate_white')
|
||||
|
||||
def test_uniform_lighting_correction(self):
|
||||
non_uniform_sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
|
||||
uniform_sequence = correct_non_uniform_lighting(non_uniform_sequence, 'DM300_nofilter_vis', white_estimator=WhiteEstimator(open_size=75, close_size=75, average_size=75)) # pylint: disable=unused-variable
|
||||
# def test_uniform_lighting_correction(self):
|
||||
# non_uniform_sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
|
||||
# uniform_sequence = correct_non_uniform_lighting(non_uniform_sequence, 'DM300_nofilter_vis', white_estimator=WhiteEstimator(open_size=75, close_size=75, average_size=75)) # pylint: disable=unused-variable
|
||||
|
||||
def test_template_matcher(self):
|
||||
sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
|
||||
stack = sequence.as_hyperstack(['DM300_nofilter_vis'], selected_frames=[0])
|
||||
first_image = stack.get_image(frame_index=0)
|
||||
x_min = 423
|
||||
x_max = 553
|
||||
y_min = 419
|
||||
y_max = 533
|
||||
template_trap_aabb = Aabb(x_min, y_min, x_max, y_max)
|
||||
template_trap_image = first_image.get_subimage(template_trap_aabb)
|
||||
for image in [first_image, template_trap_image]:
|
||||
print(image.get_pixel_type(), image.get_width(), image.get_height())
|
||||
# the typical value of peaks is -2.e10 and the value between peaks is below -8.0e10
|
||||
threshold = -3.0e10
|
||||
tolerance = 1.0e10
|
||||
maxima_finder = MaximaFinder(threshold, tolerance)
|
||||
template_matcher = TemplateMatcher(maxima_finder)
|
||||
matches = template_matcher.match_template(first_image, template_trap_image)
|
||||
num_traps = len(matches)
|
||||
print("number of traps found : %d" % num_traps)
|
||||
num_expected_traps = 13 # 13 traps are completely visible in the first image
|
||||
self.assertAlmostEqual(len(matches), num_expected_traps, delta=1.0)
|
||||
# def test_template_matcher(self):
|
||||
# sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
|
||||
# stack = sequence.as_hyperstack(['DM300_nofilter_vis'], selected_frames=[0])
|
||||
# first_image = stack.get_image(frame_index=0)
|
||||
# x_min = 423
|
||||
# x_max = 553
|
||||
# y_min = 419
|
||||
# y_max = 533
|
||||
# template_trap_aabb = Aabb(x_min, y_min, x_max, y_max)
|
||||
# template_trap_image = first_image.get_subimage(template_trap_aabb)
|
||||
# for image in [first_image, template_trap_image]:
|
||||
# print(image.get_pixel_type(), image.get_width(), image.get_height())
|
||||
# # the typical value of peaks is -2.e10 and the value between peaks is below -8.0e10
|
||||
# threshold = -3.0e10
|
||||
# tolerance = 1.0e10
|
||||
# maxima_finder = MaximaFinder(threshold, tolerance)
|
||||
# template_matcher = TemplateMatcher(maxima_finder)
|
||||
# matches = template_matcher.match_template(first_image, template_trap_image)
|
||||
# num_traps = len(matches)
|
||||
# print("number of traps found : %d" % num_traps)
|
||||
# num_expected_traps = 13 # 13 traps are completely visible in the first image
|
||||
# self.assertAlmostEqual(len(matches), num_expected_traps, delta=1.0)
|
||||
|
||||
|
||||
def test_traps_detector(self):
|
||||
# the typical value of peaks is -500 and the value between peaks is below -2500
|
||||
threshold = -1500.0
|
||||
tolerance = 1500
|
||||
maxima_finder = MaximaFinder(threshold, tolerance)
|
||||
template_matcher = TemplateMatcher(maxima_finder)
|
||||
traps_detector = TrapsDetector(template_matcher)
|
||||
sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
|
||||
x_min = 423
|
||||
x_max = 553
|
||||
y_min = 419
|
||||
y_max = 533
|
||||
trap_aabb = Aabb(x_min, y_min, x_max, y_max)
|
||||
traps_mask = traps_detector.compute_traps_mask(sequence, 'DM300_nofilter_vis', trap_aabb)
|
||||
measured_mean_value = traps_mask.get_mean_value()
|
||||
expected_traps_coverage = 0.07909
|
||||
traps_pixel_value = 255.0
|
||||
expected_mean_value = expected_traps_coverage * traps_pixel_value
|
||||
print("expected_mean_value: %f" % expected_mean_value)
|
||||
print("measured_mean_value: %f" % measured_mean_value)
|
||||
self.assertAlmostEqual(measured_mean_value, expected_mean_value, delta=0.01)
|
||||
# def test_traps_detector(self):
|
||||
# # the typical value of peaks is -500 and the value between peaks is below -2500
|
||||
# threshold = -1500.0
|
||||
# tolerance = 1500
|
||||
# maxima_finder = MaximaFinder(threshold, tolerance)
|
||||
# template_matcher = TemplateMatcher(maxima_finder)
|
||||
# traps_detector = TrapsDetector(template_matcher)
|
||||
# sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
|
||||
# x_min = 423
|
||||
# x_max = 553
|
||||
# y_min = 419
|
||||
# y_max = 533
|
||||
# trap_aabb = Aabb(x_min, y_min, x_max, y_max)
|
||||
# traps_mask = traps_detector.compute_traps_mask(sequence, 'DM300_nofilter_vis', trap_aabb)
|
||||
# measured_mean_value = traps_mask.get_mean_value()
|
||||
# expected_traps_coverage = 0.07909
|
||||
# traps_pixel_value = 255.0
|
||||
# expected_mean_value = expected_traps_coverage * traps_pixel_value
|
||||
# print("expected_mean_value: %f" % expected_mean_value)
|
||||
# print("measured_mean_value: %f" % measured_mean_value)
|
||||
# self.assertAlmostEqual(measured_mean_value, expected_mean_value, delta=0.01)
|
||||
|
||||
def test_visible_traps_sequence_processing(self):
|
||||
# def test_visible_traps_sequence_processing(self):
|
||||
# traps_sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
|
||||
# visible_traps_sequence = traps_sequence.as_hyperstack(['DM300_nofilter_vis'])
|
||||
# background_estimator = EmptyFrameBackgroundEstimator(empty_frame_index=39)
|
||||
# processor = GlobulesAreaEstimator(background_estimator=background_estimator, particle_threshold=2000.0)
|
||||
# results = processor.detect_particles(visible_traps_sequence)
|
||||
# save_hdf5_file('results.h5', results)
|
||||
# # results file could be checked with "h5dump --xml ./lipase.git/results.h5"
|
||||
# first_frame_measured_ratio = results['globules_area_ratio'][(0,)]
|
||||
# first_frame_expected_ratio = 0.008
|
||||
# self.assertAlmostEqual(first_frame_measured_ratio, first_frame_expected_ratio, delta=0.01)
|
||||
|
||||
def test_circle_detector(self):
|
||||
traps_sequence = self.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']
|
||||
visible_traps_sequence = traps_sequence.as_hyperstack(['DM300_nofilter_vis'])
|
||||
background_estimator = EmptyFrameBackgroundEstimator(empty_frame_index=39)
|
||||
processor = GlobulesAreaEstimator(background_estimator=background_estimator, particle_threshold=2000.0)
|
||||
results = processor.detect_particles(visible_traps_sequence)
|
||||
save_hdf5_file('results.h5', results)
|
||||
# results file could be checked with "h5dump --xml ./lipase.git/results.h5"
|
||||
first_frame_measured_ratio = results['globules_area_ratio'][(0,)]
|
||||
first_frame_expected_ratio = 0.008
|
||||
self.assertAlmostEqual(first_frame_measured_ratio, first_frame_expected_ratio, delta=0.01)
|
||||
|
||||
src_image = visible_traps_sequence.get_image(frame_index=0)
|
||||
ie = IImageEngine.get_instance()
|
||||
detector = CircularSymmetryDetector(max_radius=10.0)
|
||||
radial_profiles = detector.compute_radial_profiles(src_image)
|
||||
|
||||
# def test_lipase_process(self):
|
||||
# lipase = Lipase(self.catalog, debugger=NullDebugger())
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue