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lipase
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now the code shows more clearly what it intends to do : attempts to find the white reference.

This commit is contained in:
Guillaume Raffy 2019-07-16 11:48:39 +02:00
parent 21c0fd56ad
commit 57b3f2e074
1 changed files with 24 additions and 15 deletions
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39
lipase.py
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@ -287,6 +287,8 @@ class Lipase(object):
src_median_value = self.get_image_median_value(src_image) src_median_value = self.get_image_median_value(src_image)
normalized_src_processor = src_image.getProcessor().convertToFloat() normalized_src_processor = src_image.getProcessor().convertToFloat()
normalized_src_processor.multiply(1.0 / src_median_value) normalized_src_processor.multiply(1.0 / src_median_value)
best_diff = None
best_z_index = None
for z_index in range(white_sequence.num_slices): for z_index in range(white_sequence.num_slices):
white_image_file_path = white_sequence.get_image_file_path(channel_index=0, frame_index=0, z_index=z_index) white_image_file_path = white_sequence.get_image_file_path(channel_index=0, frame_index=0, z_index=z_index)
white_image = IJ.openImage(white_image_file_path) white_image = IJ.openImage(white_image_file_path)
@ -306,8 +308,8 @@ class Lipase(object):
difference_image = ic.run("sub create float", normalized_src, normalized_white) difference_image = ic.run("sub create float", normalized_src, normalized_white)
# self.debugger.on_image(imp3, 'diff') # self.debugger.on_image(imp3, 'diff')
self.debugger.on_image(normalized_white, 'normalized_white') # self.debugger.on_image(normalized_white, 'normalized_white')
self.debugger.on_image(difference_image, 'difference_image') # self.debugger.on_image(difference_image, 'difference_image')
# imp2mat = ImagePlusMatConverter() # imp2mat = ImagePlusMatConverter()
# white_mat = imp2mat.toMat(white_image.getProcessor()) # white_mat = imp2mat.toMat(white_image.getProcessor())
@ -316,6 +318,10 @@ class Lipase(object):
sqdiff_image = ic.run("mul create float", difference_image, difference_image) sqdiff_image = ic.run("mul create float", difference_image, difference_image)
mean_sqdiff = self.get_image_mean_value(sqdiff_image) mean_sqdiff = self.get_image_mean_value(sqdiff_image)
print('difference : ', mean_sqdiff) print('difference : ', mean_sqdiff)
if best_diff is None or mean_sqdiff < best_diff:
best_diff = mean_sqdiff
best_z_index = z_index
return best_z_index
def compute_sequence_median_image(self, sequence, channel_id='DM300_nofilter_vis'): def compute_sequence_median_image(self, sequence, channel_id='DM300_nofilter_vis'):
''' computes for each pixel its median value along time, so that in the end we have a single image that only shows structures (things that don't move such as the traps) ''' computes for each pixel its median value along time, so that in the end we have a single image that only shows structures (things that don't move such as the traps)
@ -336,27 +342,30 @@ class Lipase(object):
background_image.show() background_image.show()
return background_image return background_image
def test_uniformization(self, sequence):
white_seq = sequence.get_white()
channel_index = sequence.get_channel_index('DM300_327-353_fluo')
src_image_file_path = sequence.get_image_file_path(channel_index=channel_index, frame_index=0, z_index=0)
src_image = IJ.openImage(src_image_file_path)
# src_image = IJ.openImage(src_image_file_path)
self.find_depth_index(src_image, white_seq)
def process_sequence(self, sequence_id): def process_sequence(self, sequence_id):
''' '''
:param str sequence_id: :param str sequence_id:
''' '''
sequence = self.catalog.sequences[sequence_id] raise NotImplementedError()
self.extract_background(sequence)
self.test_uniformization(sequence)
def test_find_white():
lipase = Lipase(debugger=ImageLogger())
sequence = lipase.catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']
white_seq = sequence.get_white()
channel_index = sequence.get_channel_index('DM300_327-353_fluo')
src_image_file_path = sequence.get_image_file_path(channel_index=channel_index, frame_index=0, z_index=0)
src_image = IJ.openImage(src_image_file_path)
# src_image = IJ.openImage(src_image_file_path)
depth_index = lipase.find_depth_index(src_image, white_seq)
def run_script(): def run_script():
lipase = Lipase(debugger=ImageLogger()) test_find_white()
lipase.process_sequence('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2')
if False:
lipase = Lipase(debugger=ImageLogger())
lipase.process_sequence('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2')
if False: if False:
sequence = lipase.catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0'] sequence = lipase.catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']