refactoring: renamed width() into get_width() to avoid confusion with properties
This commit is contained in:
Guillaume Raffy
parent
777db445be
commit
df1a9b869f
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@ -47,11 +47,11 @@ class IImage(ABC):
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pass
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@abc.abstractmethod
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def width(self):
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def get_width(self):
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pass
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@abc.abstractmethod
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def height(self):
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def get_height(self):
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pass
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@abc.abstractmethod
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@ -93,11 +93,11 @@ class IImage(ABC):
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class IHyperStack(ABC):
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@abc.abstractmethod
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def width(self):
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def get_width(self):
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pass
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@abc.abstractmethod
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def height(self):
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def get_height(self):
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pass
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@abc.abstractmethod
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@ -160,7 +160,7 @@ class IImageFeeder(ABC):
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image = it.next()
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ie = IImageEngine.get_instance()
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hyperstack = ie.create_hyperstack(width=image.width(), height=image.height(), num_channels=1, num_slices=1, num_frames=self.get_num_images(), pixel_type=image.get_pixel_type())
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hyperstack = ie.create_hyperstack(width=image.get_width(), height=image.get_height(), num_channels=1, num_slices=1, num_frames=self.get_num_images(), pixel_type=image.get_pixel_type())
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frame_index = 0
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for image in it:
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hyperstack.set_image(image, frame_index=frame_index)
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@ -46,7 +46,7 @@ class IJImage(IImage):
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def clone(self, clone_pixel_type=None):
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if clone_pixel_type == None:
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clone_pixel_type = self.get_pixel_type()
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copy = IJImage(self.image_engine, width=self.width(), height=self.height(), pixel_type=clone_pixel_type)
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copy = IJImage(self.image_engine, width=self.get_width(), height=self.get_height(), pixel_type=clone_pixel_type)
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src_processor = self.ij_image.getProcessor()
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clone_processor = {
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PixelType.U8: src_processor.convertToByteProcessor(),
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@ -57,10 +57,10 @@ class IJImage(IImage):
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assert copy.get_pixel_type() == clone_pixel_type
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return copy
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def width(self):
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def get_width(self):
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return self.ij_image.width
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def height(self):
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def get_height(self):
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return self.ij_image.height
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def get_pixel_type(self):
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@ -113,15 +113,15 @@ class IJHyperStack(IHyperStack):
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def get_image(self, frame_index=0, slice_index=0, channel_index=0):
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self.hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
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stack_name = ''
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image_plus = IJ.createHyperStack(stack_name, self.width(), self.height(), 1, 1, 1, PixelType.get_num_bits(self.get_pixel_type()))
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image_plus = IJ.createHyperStack(stack_name, self.get_width(), self.get_height(), 1, 1, 1, PixelType.get_num_bits(self.get_pixel_type()))
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image_plus.setProcessor(self.hyperstack.getProcessor())
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ij_image = IJImage(self.image_engine, image_plus)
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return ij_image
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def width(self):
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def get_width(self):
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return self.hyperstack.width
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def height(self):
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def get_height(self):
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return self.hyperstack.height
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def num_slices(self):
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@ -334,7 +334,7 @@ class IJImageEngine(IImageEngine):
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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_template_image = imp2mat.toMat(template_image.ij_image.getProcessor())
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similarity_image_size = opencv_core.Size(src_image.width()-template_image.width()+1, src_image.width()-template_image.height()+1)
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similarity_image_size = opencv_core.Size(src_image.get_width()-template_image.get_width()+1, src_image.get_width()-template_image.get_height()+1)
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cv_similarity_image = opencv_core.Mat(similarity_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 cvMatchTemplate 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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@ -363,8 +363,8 @@ class IJImageEngine(IImageEngine):
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# print(cv_similarity_image)
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similarity_image = self.create_image(
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width=src_image.width()-template_image.width()+1,
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height=src_image.height()-template_image.height()+1,
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width=src_image.get_width()-template_image.get_width()+1,
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height=src_image.get_height()-template_image.get_height()+1,
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pixel_type=PixelType.F32)
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mat2imp = MatImagePlusConverter()
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@ -178,7 +178,7 @@ def correct_non_uniform_lighting(non_uniform_sequence, channel_id, white_estimat
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ie = IImageEngine.get_instance()
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white_estimate = white_estimator.estimate_white([non_uniform_sequence], [channel_id])
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uniform_stack = ie.create_hyperstack(width=white_estimate.width(), height=white_estimate.height(), num_slices=1, num_frames=non_uniform_sequence.num_frames, num_channels=1, pixel_type=PixelType.F32)
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uniform_stack = ie.create_hyperstack(width=white_estimate.get_width(), height=white_estimate.get_height(), num_slices=1, num_frames=non_uniform_sequence.num_frames, num_channels=1, pixel_type=PixelType.F32)
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for frame_index in range(non_uniform_sequence.num_frames):
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non_uniform_frame = ie.load_image(non_uniform_sequence.get_image_file_path(channel_index=0, frame_index=frame_index, slice_index=0))
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@ -221,7 +221,7 @@ def correct_non_uniform_lighting(non_uniform_sequence, channel_id, white_estimat
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# :return IHyperStack: the hyperstack of images after correction
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# """
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# white_estimate = white_estimator.estimate_white([non_uniform_sequence], [channel_id])
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# uniform_stack = IImageEngine.get_instance().create_hyperstack(width=white_estimate.width(), height=white_estimate.height(), num_slices=1, num_frames=non_uniform_sequence.num_frames, num_channels=1, pixel_type=PixelType.F32)
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# uniform_stack = IImageEngine.get_instance().create_hyperstack(width=white_estimate.get_width(), height=white_estimate.get_height(), num_slices=1, num_frames=non_uniform_sequence.num_frames, num_channels=1, pixel_type=PixelType.F32)
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# for frame_index in range(non_uniform_sequence.num_frames):
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# non_uniform_frame = IImageEngine.get_instance().load_image(non_uniform_sequence.get_image_file_path(channel_index=0, frame_index=frame_index, slice_index=0))
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@ -107,7 +107,7 @@ class TrapsDetector(object):
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binarizer = TrapBinarizer((70,34))
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trap_mask = binarizer.binarize_trap(clean_trap_image)
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traps_mask = ie.create_image(width=uniform_stack.width(), height=uniform_stack.height(), pixel_type=uniform_stack.get_pixel_type())
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traps_mask = ie.create_image(width=uniform_stack.get_width(), height=uniform_stack.get_height(), pixel_type=uniform_stack.get_pixel_type())
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for frame_trap_index in range(num_traps_per_frame):
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match = matches[frame_trap_index]
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traps_mask.set_subimage(trap_mask, (match.x, match.y))
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@ -56,7 +56,7 @@ class TestLipase(unittest.TestCase):
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template_trap_aabb = Aabb(x_min, y_min, x_max, y_max)
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template_trap_image = first_image.get_subimage(template_trap_aabb)
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for image in [first_image, template_trap_image]:
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print(image.get_pixel_type(), image.width(), image.height())
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print(image.get_pixel_type(), image.get_width(), image.get_height())
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# the typical value of peaks is -2.e10 and the value between peaks is below -8.0e10
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threshold = -3.0e10
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tolerance = 1.0e10
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