refactor : moved catalog code in a separate module
This commit is contained in:
parent
57b3f2e074
commit
76607c19fc
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@ -0,0 +1,159 @@
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import json
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class Sequence(object):
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def __init__(self, catalog, sequence_id, micro_manager_metadata_file_path):
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self.catalog = catalog
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self.sequence_id = sequence_id
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self.micro_manager_metadata_file_path = micro_manager_metadata_file_path
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print(micro_manager_metadata_file_path)
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with open(micro_manager_metadata_file_path, "r") as mmm_file:
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self.mmm = json.load(mmm_file, encoding='latin-1') # note : the micromanager metadata files are encoded in latin-1, not utf8 (see accents in comments)
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@property
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def num_frames(self):
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summary = self.mmm['Summary']
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return int(summary['Frames'])
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@property
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def width(self):
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summary = self.mmm['Summary']
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return int(summary['Width'])
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@property
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def height(self):
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summary = self.mmm['Summary']
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return int(summary['Height'])
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@property
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def num_channels(self):
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summary = self.mmm['Summary']
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return int(summary['Channels'])
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@property
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def num_slices(self):
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summary = self.mmm['Summary']
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return int(summary['Slices'])
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@property
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def num_bits_per_pixels(self):
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summary = self.mmm['Summary']
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return int(summary['BitDepth'])
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def get_root_path(self):
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return '/'.join(self.micro_manager_metadata_file_path.split('/')[:-1])
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def get_image_file_path(self, channel_index, frame_index, z_index=0):
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'''
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:param int channel_index:
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:param int frame_index:
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:param int z_index:
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'''
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assert frame_index < self.num_frames
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assert channel_index < self.num_channels
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frame_info = self.mmm['FrameKey-%d-%d-%d' % (frame_index, channel_index, z_index)]
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rel_file_path = frame_info['FileName']
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return self.get_root_path() + '/' + rel_file_path
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def get_channel_index(self, channel_id):
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'''
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:param str channel_id:
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'''
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summary = self.mmm['Summary']
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channel_index = summary['ChNames'].index(channel_id)
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return channel_index
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def get_black(self):
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''' returns the black sequence related to the the sequence self
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:return Sequence:
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'''
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seqid_to_black = {
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0': 'res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0',
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2': 'res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0',
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}
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white_sequence = seqid_to_black[self.sequence_id]
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return self.catalog.sequences[white_sequence]
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def get_white(self):
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''' returns the white sequence related to the the sequence self
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:return Sequence:
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'''
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# assert fixme : res_soleil2018/white/white_24112018_2/Pos0 is visible
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seqid_to_white = {
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0': 'res_soleil2018/white/white_24112018_2/Pos0',
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2': 'res_soleil2018/white/white_24112018_2/Pos0',
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}
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white_sequence = seqid_to_white[self.sequence_id]
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return self.catalog.sequences[white_sequence]
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def as_hyperstack(self):
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hyperstack = IJ.createHyperStack(self.sequence_id, self.width, self.height, self.num_channels, self.num_slices, self.num_frames, self.num_bits_per_pixels)
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for channel_index in range(self.num_channels):
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for frame_index in range(self.num_frames):
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slice_index = 0
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src_image_file_path = self.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
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# print(src_image_file_path)
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src_image = IJ.openImage(src_image_file_path)
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# print(src_image.getProperties())
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hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
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hyperstack.setProcessor(src_image.getProcessor())
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return hyperstack
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def as_stack(self, channel_id):
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'''
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:param str channel_id: eg 'DM300_327-353_fluo'
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'''
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channel_index = self.get_channel_index(channel_id)
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hyperstack = IJ.createHyperStack(self.sequence_id, self.width, self.height, 1, self.num_slices, self.num_frames, self.num_bits_per_pixels)
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for frame_index in range(self.num_frames):
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slice_index = 0
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src_image_file_path = self.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
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# print(src_image_file_path)
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src_image = IJ.openImage(src_image_file_path)
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# print(src_image.getProperties())
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hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
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hyperstack.setProcessor(src_image.getProcessor())
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return hyperstack
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def open_in_imagej(self):
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# ip = IJ.createHyperStack(title=self.sequence_id, width=self.width, height= self.height, channels=1, slices=1, frames=self.get_num_frames(), bitdepth=16)
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hyperstack = self.as_hyperstack()
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hyperstack.show()
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for channel_index in range(self.num_channels):
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hyperstack.setPositionWithoutUpdate(channel_index + 1, 1, 1)
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IJ.run("Enhance Contrast", "saturated=0.35")
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return hyperstack
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class ImageCatalog(object):
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def __init__(self, raw_images_root):
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self.raw_images_root = raw_images_root
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self.sequences = {}
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# nb : we use the path as sequence id because the "Comment" field in the summary section of the metadata file is not guaranteed to be unique (eg they are the same in res_soleil2018/white/white_24112018_1/Pos0 and in res_soleil2018/white/white_24112018_2/Pos0)
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sequence_ids = []
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sequence_ids.append('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0')
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sequence_ids.append('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2')
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sequence_ids.append('res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0')
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sequence_ids.append('res_soleil2018/DARK/DARK_40X_zstack_vis_327-353_1/Pos0')
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# sequence_ids.append('res_soleil2018/white/white_24112018_1/Pos0') # this sequence seems broken (only 5 images while there's supposed to be 201 frames)
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sequence_ids.append('res_soleil2018/white/white_24112018_2/Pos0')
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for sequence_id in sequence_ids:
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micro_manager_metadata_file_path = raw_images_root + '/' + sequence_id + '/metadata.txt'
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# micro_manager_metadata_file_path = '/tmp/toto.json'
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self.sequences[sequence_id] = Sequence(self, sequence_id, micro_manager_metadata_file_path)
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def __str__(self):
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for sequence_id, sequence in self.sequences.iteritems():
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return str(sequence_id) + ':' + str(sequence)
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# self.add_micromanager_metadata(raw_images_root + '/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/metadata.txt')
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# def add_micromanager_metadata(self, micro_manager_metadata_file_path):
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# self.sequences[ micro_manager_metadata_file_path ] = Sequence(self, micro_manager_metadata_file_path)
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188
lipase.py
188
lipase.py
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@ -1,5 +1,10 @@
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# note: fiji's jython doesn't support encoding keyword
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# String(label="Please enter your name",description="Name field") name
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# OUTPUT String greeting
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import sys
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print(sys.version) # prints python version
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sys.path.append('/Users/graffy/ownCloud/ipr/lipase/lipase.git') # necessary if run from fiji as script otherwise jython fails to find lipase's modules such as catalog
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# A Jython script with parameters.
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# It is the duty of the scripting framework to harvest
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@ -12,7 +17,7 @@ from ij.process import ImageStatistics
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from ij.plugin import ImageCalculator
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from ij.plugin import ZProjector
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from ij import WindowManager
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from catalog import Sequence, ImageCatalog
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# greeting = "Hello, " + name + "!"
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@ -40,164 +45,6 @@ from ij import WindowManager
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# 90mn : on fait un stack -> phiG_I_40x_Zstack20um_1
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# - cin2 : autre échantillon similaire à cin1
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# - cond[5678] : condition non réalistes
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import json
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class Sequence(object):
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def __init__(self, catalog, sequence_id, micro_manager_metadata_file_path):
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self.catalog = catalog
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self.sequence_id = sequence_id
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self.micro_manager_metadata_file_path = micro_manager_metadata_file_path
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print(micro_manager_metadata_file_path)
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with open(micro_manager_metadata_file_path, "r") as mmm_file:
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self.mmm = json.load(mmm_file, encoding='latin-1') # note : the micromanager metadata files are encoded in latin-1, not utf8 (see accents in comments)
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@property
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def num_frames(self):
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summary = self.mmm['Summary']
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return int(summary['Frames'])
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@property
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def width(self):
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summary = self.mmm['Summary']
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return int(summary['Width'])
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@property
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def height(self):
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summary = self.mmm['Summary']
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return int(summary['Height'])
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@property
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def num_channels(self):
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summary = self.mmm['Summary']
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return int(summary['Channels'])
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@property
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def num_slices(self):
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summary = self.mmm['Summary']
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return int(summary['Slices'])
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@property
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def num_bits_per_pixels(self):
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summary = self.mmm['Summary']
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return int(summary['BitDepth'])
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def get_root_path(self):
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return '/'.join(self.micro_manager_metadata_file_path.split('/')[:-1])
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def get_image_file_path(self, channel_index, frame_index, z_index=0):
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'''
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:param int channel_index:
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:param int frame_index:
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:param int z_index:
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'''
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assert frame_index < self.num_frames
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assert channel_index < self.num_channels
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frame_info = self.mmm['FrameKey-%d-%d-%d' % (frame_index, channel_index, z_index)]
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rel_file_path = frame_info['FileName']
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return self.get_root_path() + '/' + rel_file_path
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def get_channel_index(self, channel_id):
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'''
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:param str channel_id:
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'''
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summary = self.mmm['Summary']
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channel_index = summary['ChNames'].index(channel_id)
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return channel_index
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def get_black(self):
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''' returns the black sequence related to the the sequence self
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:return Sequence:
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'''
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seqid_to_black = {
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0': 'res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0',
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2': 'res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0',
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}
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white_sequence = seqid_to_black[self.sequence_id]
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return self.catalog.sequences[white_sequence]
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def get_white(self):
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''' returns the white sequence related to the the sequence self
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:return Sequence:
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'''
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# assert fixme : res_soleil2018/white/white_24112018_2/Pos0 is visible
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seqid_to_white = {
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0': 'res_soleil2018/white/white_24112018_2/Pos0',
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'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2': 'res_soleil2018/white/white_24112018_2/Pos0',
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}
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white_sequence = seqid_to_white[self.sequence_id]
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return self.catalog.sequences[white_sequence]
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def as_hyperstack(self):
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hyperstack = IJ.createHyperStack(self.sequence_id, self.width, self.height, self.num_channels, self.num_slices, self.num_frames, self.num_bits_per_pixels)
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for channel_index in range(self.num_channels):
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for frame_index in range(self.num_frames):
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slice_index = 0
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src_image_file_path = self.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
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# print(src_image_file_path)
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src_image = IJ.openImage(src_image_file_path)
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# print(src_image.getProperties())
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hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
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hyperstack.setProcessor(src_image.getProcessor())
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return hyperstack
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def as_stack(self, channel_id):
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'''
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:param str channel_id: eg 'DM300_327-353_fluo'
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'''
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channel_index = self.get_channel_index(channel_id)
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hyperstack = IJ.createHyperStack(self.sequence_id, self.width, self.height, 1, self.num_slices, self.num_frames, self.num_bits_per_pixels)
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for frame_index in range(self.num_frames):
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slice_index = 0
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src_image_file_path = self.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
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# print(src_image_file_path)
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src_image = IJ.openImage(src_image_file_path)
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# print(src_image.getProperties())
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hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
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hyperstack.setProcessor(src_image.getProcessor())
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return hyperstack
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def open_in_imagej(self):
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# ip = IJ.createHyperStack(title=self.sequence_id, width=self.width, height= self.height, channels=1, slices=1, frames=self.get_num_frames(), bitdepth=16)
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hyperstack = self.as_hyperstack()
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hyperstack.show()
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for channel_index in range(self.num_channels):
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hyperstack.setPositionWithoutUpdate(channel_index + 1, 1, 1)
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IJ.run("Enhance Contrast", "saturated=0.35")
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return hyperstack
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class ImageCatalog(object):
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def __init__(self, raw_images_root):
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self.raw_images_root = raw_images_root
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self.sequences = {}
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# nb : we use the path as sequence id because the "Comment" field in the summary section of the metadata file is not guaranteed to be unique (eg they are the same in res_soleil2018/white/white_24112018_1/Pos0 and in res_soleil2018/white/white_24112018_2/Pos0)
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sequence_ids = []
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sequence_ids.append('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0')
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sequence_ids.append('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2')
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sequence_ids.append('res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0')
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sequence_ids.append('res_soleil2018/DARK/DARK_40X_zstack_vis_327-353_1/Pos0')
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# sequence_ids.append('res_soleil2018/white/white_24112018_1/Pos0') # this sequence seems broken (only 5 images while there's supposed to be 201 frames)
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sequence_ids.append('res_soleil2018/white/white_24112018_2/Pos0')
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for sequence_id in sequence_ids:
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micro_manager_metadata_file_path = raw_images_root + '/' + sequence_id + '/metadata.txt'
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# micro_manager_metadata_file_path = '/tmp/toto.json'
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self.sequences[sequence_id] = Sequence(self, sequence_id, micro_manager_metadata_file_path)
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def __str__(self):
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for sequence_id, sequence in self.sequences.iteritems():
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return str(sequence_id) + ':' + str(sequence)
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# self.add_micromanager_metadata(raw_images_root + '/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/metadata.txt')
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# def add_micromanager_metadata(self, micro_manager_metadata_file_path):
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# self.sequences[ micro_manager_metadata_file_path ] = Sequence(self, micro_manager_metadata_file_path)
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class IImageProcessingDebugger(object):
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@ -234,18 +81,12 @@ class ImageLogger(IImageProcessingDebugger):
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class Lipase(object):
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def __init__(self, debugger=NullDebugger()):
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def __init__(self, catalog, debugger=NullDebugger()):
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'''
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:param IImageProcessingDebugger im_proc_debugger:
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'''
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self.catalog = catalog
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self.debugger = debugger
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raw_images_root = '/Users/graffy/ownCloud/ipr/lipase/raw-images'
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self.catalog = ImageCatalog(raw_images_root)
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print(self.catalog)
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# catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0'].open_in_imagej()
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# catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2'].open_in_imagej()
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# catalog.sequences['DARK_40X_60min_1 im pae min_1/Pos0'].open_in_imagej()
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# catalog.sequences['white_24112018_1/Pos0'].open_in_imagej()
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def get_image_median_value(self, src_image):
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'''
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@ -350,7 +191,16 @@ class Lipase(object):
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def test_find_white():
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lipase = Lipase(debugger=ImageLogger())
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raw_images_root = '/Users/graffy/ownCloud/ipr/lipase/raw-images'
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catalog = ImageCatalog(raw_images_root)
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print(catalog)
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# catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0'].open_in_imagej()
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# catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2'].open_in_imagej()
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# catalog.sequences['DARK_40X_60min_1 im pae min_1/Pos0'].open_in_imagej()
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# catalog.sequences['white_24112018_1/Pos0'].open_in_imagej()
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|
||||
lipase = Lipase(catalog, 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')
|
||||
|
|
@ -364,7 +214,7 @@ def run_script():
|
|||
test_find_white()
|
||||
|
||||
if False:
|
||||
lipase = Lipase(debugger=ImageLogger())
|
||||
lipase = Lipase(ImageCatalog('/Users/graffy/ownCloud/ipr/lipase/raw-images'), debugger=ImageLogger())
|
||||
lipase.process_sequence('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2')
|
||||
|
||||
if False:
|
||||
|
|
|
|||
Loading…
Reference in New Issue